Clinical Programmer II Salary in the United States
How much does a Clinical Programmer II make in the United States?
As of July 01, 2026, the average salary for a Clinical Programmer II in the United States is $97,974 per year, which breaks down to an hourly rate of $47.
However, a Clinical Programmer II's salary can vary significantly. Here’s a look at the typical salary range:
Top Earners (90th percentile): $113,600
Majority Range (25th-75th percentile): $88,828 to $106,153
Key Factors That Influence Clinical Programmer II Salaries
A Clinical Programmer II's salary isn't a fixed number.
It's shaped by several important factors.
Below, we'll explore how your years of experience, geographic location, education, and company size can directly affect your earning potential.
How Experience Level Affects Clinical Programmer Salaries?
Experience is a primary driver of a Clinical Programmer II's salary.
As you build your skills and take on more complex tasks, your compensation generally increases.
Here's how the average salary grows at different career stages:
Clinical Programmer I (0-2 years): $72,184
Clinical Programmer II (2-4 years): $97,974
Clinical Programmer III (4-7 years): $107,701
Clinical Programmer IV (7+ years): $134,777
Job Role
Years of Experience
Average Salary
Clinical Programmer I
0-2 years
$72,184
Clinical Programmer II
2-4 years
$97,974
Clinical Programmer III
4-7 years
$107,701
Clinical Programmer IV
7+ years
$134,777
$72,184Clinical ...
$97,974Clinical ...
$107,701Clinical ...
$134,777Clinical ...
View as Table
View as Graph
What Am I Worth?
How Do Clinical Programmer II Salaries Vary from State to State?
Your salary can change significantly depending on where you work.
States with a higher cost of living and strong industrial sectors
often pay more to attract Clinical Programmer IIs.
For example, consider the average annual salaries in these key locations:
District of Columbia: $108,477.
California: $108,065.
Massachusetts: $106,625.
District of Columbia$108,477
California$108,065
Massachusetts$106,625
Washington$106,233
New Jersey$106,194
Alaska$106,057
Connecticut$104,705
New York$104,156
Hawaii$102,402
Rhode Island$101,579
Maryland$101,021
Minnesota$100,257
Colorado$99,963
Illinois$99,865
Oregon$99,493
Delaware$99,218
New Hampshire$99,046
Virginia$98,660
Pennsylvania$97,533
Nevada$96,965
North Dakota$96,779
Michigan$96,485
Wisconsin$96,377
Vermont$96,161
Texas$95,564
Maine$95,525
Arizona$95,466
Ohio$95,397
Georgia$94,496
Indiana$94,045
Wyoming$93,957
Utah$93,820
Iowa$93,761
Kansas$93,291
Louisiana$93,154
North Carolina$93,105
Missouri$93,085
Florida$92,703
Montana$92,497
Nebraska$92,301
Kentucky$92,194
South Carolina$91,802
Tennessee$91,557
Idaho$91,459
New Mexico$90,744
Oklahoma$90,587
Alabama$90,009
South Dakota$89,039
Arkansas$88,510
West Virginia$88,226
Mississippi$87,373
Top Paying Cities for Clinical Programmer IIs
Salaries can also vary between different cities.
Major metropolitan areas or cities with a high demand for technicians often offer more competitive pay.
Here are a few examples of average annual salaries in different U.S. cities:
San Jose: $123,575
San Francisco: $122,222
Oakland: $119,646
San Jose, CA$123,575
San Francisco, CA$122,222
Oakland, CA$119,646
New York, NY$112,806
Paramus, NJ$111,435
Queens Village, NY$111,430
Passaic, NJ$111,337
Bergenfield, NJ$111,328
Stamford, CT$111,112
Huntington, NY$111,072
Newark, NJ$110,348
Bridgeport, CT$110,141
Vallejo, CA$109,946
New Brunswick, NJ$109,907
Petaluma, CA$109,848
Middlesex, NJ$109,662
Somerset, NJ$109,594
Santa Cruz, CA$109,466
Boston, MA$108,869
Monterey, CA$108,525
Seattle, WA$108,300
Santa Rosa, CA$108,281
Los Angeles, CA$108,251
Juneau, AK$107,997
Washington, DC$107,889
Orange, CA$107,540
Santa Ana, CA$107,282
Long Beach, CA$107,184
Anaheim, CA$107,164
Anchorage, AK$107,115
Santa Maria, CA$106,821
Everett, WA$106,801
Danbury, CT$106,457
Bremerton, WA$106,321
Tacoma, WA$105,969
New Suffolk, NY$105,967
Sacramento, CA$105,939
Santa Barbara, CA$105,832
Trenton, NJ$105,724
San Diego, CA$105,724
Brockton, MA$105,616
Fairbanks, AK$105,376
Lompoc, CA$105,126
Lowell, MA$105,047
Ventura, CA$105,028
Nashua, NH$105,009
Stockton, CA$104,999
Modesto, CA$104,284
Poughkeepsie, NY$104,068
Olympia, WA$103,882
Kennewick, WA$103,882
New Haven, CT$103,843
Lawrence, MA$103,490
Hartford, CT$103,392
Riverside, CA$103,372
New Bedford, MA$103,274
Richland, WA$103,274
Bakersfield, CA$103,137
San Bernardino, CA$103,098
New Britain, CT$103,088
Atlantic City, NJ$103,088
New London, CT$103,049
Norwich, CT$103,020
Portsmouth, NH$103,000
Boulder, CO$102,792
Portland, OR$102,657
Worcester, MA$102,647
Minneapolis, MN$102,344
Philadelphia, PA$102,206
Honolulu, HI$101,883
Saint Paul, MN$101,836
Vineland, NJ$101,815
Providence, RI$101,530
Chicago, IL$101,246
Bellingham, WA$101,129
Springfield, MA$101,050
Baltimore, MD$101,021
Chico, CA$100,776
Pittsfield, MA$100,512
Manchester, NH$100,325
Spokane, WA$99,894
Denver, CO$99,884
Albany, NY$99,424
Troy, NY$99,385
Nassau, NY$99,280
Schenectady, NY$99,179
Wilmington, DE$99,101
Burlington, VT$98,964
Salem, OR$98,924
Portland, ME$98,621
Yakima, WA$98,523
Rochester, MN$98,219
Reno, NV$98,170
Fresno, CA$98,170
Milwaukee, WI$98,082
Detroit, MI$97,984
Ann Arbor, MI$97,967
Allentown, PA$97,954
Colorado Springs, CO$97,788
Syracuse, NY$97,739
Carson City, NV$97,739
Houston, TX$97,602
Eugene, OR$97,553
Gary, IN$97,435
Springfield, OR$97,357
Bismarck, ND$97,337
Galveston, TX$97,269
Medford, OR$97,122
Fort Collins, CO$97,082
Concord, NH$97,033
Austin, TX$97,004
Mesa, AZ$96,798
Reading, PA$96,789
Phoenix, AZ$96,779
Dallas, TX$96,749
Saint Cloud, MN$96,655
Madison, WI$96,524
Utica, NY$96,259
Rochester, NY$96,103
Des Moines, IA$96,093
Raleigh, NC$96,083
Atlanta, GA$95,936
Battle Creek, MI$95,907
Salt Lake City, UT$95,877
Lancaster, PA$95,730
Harrisburg, PA$95,593
Kansas City, MO$95,495
Champaign, IL$95,476
Kansas City, KS$95,476
Fort Worth, TX$95,466
Columbus, OH$95,449
Boca Raton, FL$95,427
Pittsburgh, PA$95,387
Richmond, VA$95,348
Indianapolis, IN$95,329
Cleveland, OH$95,319
Las Vegas, NV$95,201
Cincinnati, OH$95,201
Petersburg, VA$95,054
Huntsville, AL$94,907
Lansing, MI$94,842
Lebanon, PA$94,829
Pueblo, CO$94,819
Appleton, WI$94,790
Buffalo, NY$94,751
Dayton, OH$94,721
Racine, WI$94,702
Charlotte, NC$94,692
Saint Louis, MO$94,662
York, PA$94,604
Elkhart, IN$94,604
Gastonia, NC$94,585
Billings, MT$94,562
Beaumont, TX$94,535
Lorain, OH$94,516
Benton Harbor, MI$94,496
Toledo, OH$94,476
Binghamton, NY$94,427
Rock Hill, SC$94,418
Rockford, IL$94,369
Springfield, IL$94,329
Elyria, OH$94,320
Fargo, ND$94,320
Flagstaff, AZ$94,251
Fort Lauderdale, FL$94,192
Duluth, MN$94,133
Miami, FL$94,133
Cheyenne, WY$94,065
Grand Forks, ND$94,065
Bangor, ME$93,849
Cedar Rapids, IA$93,742
Durham, NC$93,700
Louisville, KY$93,693
Grand Rapids, MI$93,673
Hialeah, FL$93,663
Casper, WY$93,526
Scranton, PA$93,408
New Orleans, LA$93,379
Virginia Beach, VA$93,369
Akron, OH$93,320
Peoria, IL$93,193
Sarasota, FL$93,173
Nashville, TN$93,105
Omaha, NE$93,105
Green Bay, WI$93,105
Baton Rouge, LA$93,056
Charleston, SC$93,036
Jamestown, NY$92,987
Davenport, IA$92,987
Tucson, AZ$92,938
Saint Petersburg, FL$92,879
Tampa, FL$92,860
Evansville, IN$92,801
Port Arthur, TX$92,801
Bradenton, FL$92,762
Santa Fe, NM$92,585
Orlando, FL$92,409
Clearwater, FL$92,380
Canton, OH$92,174
La Crosse, WI$92,174
Albuquerque, NM$92,115
Newport News, VA$92,105
High Point, NC$92,076
Ogden, UT$92,037
Corpus Christi, TX$91,958
Norfolk, VA$91,900
Laramie, WY$91,900
Rock Island, IL$91,841
Saginaw, MI$91,821
Jacksonville, FL$91,811
Salisbury, NC$91,792
Boise, ID$91,772
Moline, IL$91,723
Fort Myers, FL$91,694
Memphis, TN$91,674
Tulsa, OK$91,625
Waterloo, IA$91,567
Spartanburg, SC$91,469
Lincoln, NE$91,420
Fort Wayne, IN$91,400
Provo, UT$91,390
Cedar Falls, IA$91,273
San Antonio, TX$91,233
Greensboro, NC$91,194
South Bend, IN$91,184
Savannah, GA$91,077
Muskegon, MI$91,037
Birmingham, AL$91,028
Winston Salem, NC$90,980
Lake Charles, LA$90,744
Anderson, IN$90,724
Lexington, KY$90,695
Augusta, GA$90,665
Greenville, SC$90,665
Lima, OH$90,587
Wichita, KS$90,577
Tuscaloosa, AL$90,577
Columbia, SC$90,489
Springfield, OH$90,469
Asheville, NC$90,312
Bloomington, IN$90,244
Knoxville, TN$89,891
Shreveport, LA$89,881
Wilmington, NC$89,754
Roanoke, VA$89,754
Topeka, KS$89,578
Frankfort, KY$89,567
Oklahoma City, OK$89,499
Chillicothe, OH$89,460
Longview, TX$89,450
Melbourne, FL$89,440
Sioux Falls, SD$89,284
Mobile, AL$89,274
Terre Haute, IN$89,235
Altoona, PA$89,176
Amarillo, TX$89,107
Killeen, TX$89,078
Fayetteville, AR$89,000
Chattanooga, TN$88,970
Sioux City, IA$88,882
Idaho Falls, ID$88,862
Lynchburg, VA$88,784
Gainesville, FL$88,657
Portsmouth, OH$88,608
Little Rock, AR$88,588
Lafayette, LA$88,549
Youngstown, OH$88,549
Daytona Beach, FL$88,490
Clarksville, TN$88,480
Pensacola, FL$88,471
Temple, TX$88,464
Hopkinsville, KY$88,177
Erie, PA$88,157
Florence, SC$88,118
Charleston, WV$87,961
Great Falls, MT$87,912
Macon, GA$87,775
Tallahassee, FL$87,765
Fayetteville, NC$87,746
Waco, TX$87,726
Helena, MT$87,657
Pine Bluff, AR$87,620
Vincennes, IN$87,501
Lubbock, TX$87,461
Alamogordo, NM$87,403
Twin Falls, ID$87,314
Rapid City, SD$87,285
Jackson, MS$87,109
Huntington, WV$87,102
Greenville, MS$87,099
Parkersburg, WV$86,999
Montgomery, AL$86,981
Wichita Falls, TX$86,883
Springfield, MO$86,883
Biloxi, MS$86,834
Monroe, LA$86,736
Johnstown, PA$86,668
Sumter, SC$86,629
Columbus, GA$86,619
Pascagoula, MS$86,433
Abilene, TX$86,433
Kingsport, TN$86,178
Albany, GA$86,178
Gulfport, MS$86,149
Alexandria, LA$85,825
Fort Smith, AR$85,580
El Paso, TX$85,316
Las Cruces, NM$84,875
Harlingen, TX$84,626
Pocatello, ID$84,610
Florence, AL$84,483
Brownsville, TX$84,463
Mcallen, TX$84,258
Dothan, AL$84,120
Columbus, MS$83,539
Altus, OK$83,082
Lawton, OK$82,896
Pierre, SD$82,543
What Skills Can Increase a Clinical Programmer II's Salary?
Demanded Skills for the Role:
Team Management (Mentioned in 3.17% Job Postings): The ability of an individual or an organization to administer and coordinate a group of individuals to perform a task. Team management involves teamwork, communication, objective setting and performance appraisals.
Clinical Research (Mentioned in 2.7% Job Postings): Clinical research is a branch of healthcare science that determines the safety and effectiveness (efficacy) of medications, devices, diagnostic products and treatment regimens intended for human use. These may be used for prevention, treatment, diagnosis or for relieving symptoms of a disease. Clinical research is different from clinical practice. In clinical practice established treatments are used, while in clinical research evidence is collected to establish a treatment.
SOP (Mentioned in 2.22% Job Postings): SOP is A standard operating procedure is a set of step-by-step instructions compiled by an organization to help workers carry out routine operations.
See More Skills
Skills
Demand Percentage
Team Management
3.17%
Clinical Research
2.7%
SOP
2.22%
What skills can make your compensation higher?
Mastering certain specialized skills can lead to a significant increase in pay.
Here are examples of skills and the potential impact they can have on a Clinical Programmer II's salary.
UAT: Can increase your salary by up to 21%.
SOP: Can increase your salary by up to 11%.
Clinical Trial: Can increase your salary by up to 10%.
Skill
Salary
Salary % Increase
UAT
$118,549
21%
SOP
$108,751
11%
Clinical Trial
$107,771
10%
Team Management
$106,792
9%
Innovation
$105,812
8%
Project Management
$105,812
8%
Get Latest Data
Clinical Programmer II Salary by Company Size: Startups vs. Enterprise
Clinical Programmer II salary potential scales significantly with company size.
Data shows that Enterprise companies (5,000+ employees) pay the highest average salary at around $110,047.
While startup companies pay approximate $93,379.
Clinical Programmer II Salary by Company Size
Company Size
Employees
Average Salary
Startup
1~50
$93,379
Growth Stage
51~500
$98,676
Established
501~5000
$106,355
Enterprise
5000+
$110,047
Clinical Programmer II Salary by Industry: Top Paying Sectors
For Clinical Programmer II roles, the industry you choose can affect earning potential
by as much as 50% (the gap between the highest and lowest paying industries).
Data shows that the Biotechnology and Healthcare
sectors offer the strongest compensation, at 25% above the average.
In contrast, Clinical Programmer positions in Edu., Gov't. & Nonprofit or MFG Nondurable typically offer lower base pay,
as these industries often view Clinical Programmer II as a support function rather than a direct revenue driver.
The top paying industries for a Clinical Programmer II
Industry Sector
Average Annual Salary
Average Hourly Rate
Pay vs.Avg
Biotechnology
$122,468
$59.0
25%
Healthcare
$112,670
$54.0
15%
How Education impacts a Clinical Programmer II's Salary?
Your level of education can impact your salary potential.
While many Clinical Programmer IIs enter the field with a Associate's Degree degree,
higher education can lead to more specialized and higher-paying roles.
According to our 100% employer-reported salary data,
the median salary for a Clinical Programmer II with a Associate's Degree is between
$84,161
and $89,190).
Clinical Programmer II Salaries by Degree Level
Typical Education for Clinical Programmer II
No Diploma2.9%
High School31.4%
Associates2.9%
Bachelors31.4%
Masters60.0%
Doctorate5.7%
view as table
Degree Level
% of user with this level of education
No Diploma
2.9%
High School
31.4%
Associates
2.9%
Bachelors
31.4%
Masters
60.0%
Doctorate
5.7%
view as graph
Clinical Programmer II Salary: Hourly Rate, Weekly Pay, and Monthly Pay
Understanding how a Clinical Programmer II's annual salary breaks down can help with budgeting.
Below, you can see the average hourly rate, weekly pay, and monthly pay for this role.
Use the buttons to switch between different pay periods.
Hourly
Monthly
Weekly
Yearly
Table View
Last Updated on July 01, 2026
$88,828
Average$97,974/year
$106,153
$7,402
Average$8,165/month
$8,846
$1,708
Average$1,884/week
$2,041
$43
Average$47/hour
$51
Annual Salary
Monthly Pay
Weekly Pay
Hourly Wage
75th Percentile
$106,153
$8,846
$2,041
$51
Average
$97,974
$8,165
$1,884
$47
25th Percentile
$88,828
$7,402
$1,708
$43
Clinical Programmer II Salary Growth & Career Path
Promotions are the fastest way to increase your earnings.
As a Clinical Programmer II, you have the following paths for advancement.
The table below compares the salary raises for common next-step roles.
By comparing these figures, you can choose the career path that best meets your financial goals.
Clinical Programmer II Salary Growth and Career Path
Next Step Role
Estimate Salary
Projected Raise
EHR Certified Application Analyst III
$120,549
23%
Clinical Programmer III
$107,701
10%
Salaries of jobs related to Clinical Programmer II
Salaries for a Clinical Programmer II can change over time,
reflecting shifts in market demand and the overall economy.
The median salary decreased from $86,047 in 2023
to around $85,658 in 2025,
reflecting changes in demand, location, experience, and the wider economy.
For a detailed analysis of Clinical Programmer II salary trends,
.
Average Annual Salary of Clinical Programmer II Over Time
2022
$???
2023
$86,047
2024
$86,257
2025
$85,658
2026
$???
2027
$???
Year
Average Annual Salary
2022
View More
2023
$86,047
2024
$86,257
2025
$85,658
2026
View More
2027
View More
Most common benefits for Clinical Programmer II
Social Security
401(k)
Disability
Healthcare
Pension
Time Off (days)
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Common company salaries for Clinical Programmer II
Here are companies hiring for Clinical Programmer II and their salaries, click below for more details.
C
$128,509/per year
C R Bard Inc
Biotechnology
the United States
H
$124,697/per year
Henry Schein Canada
Biotechnology
the United States
N
$123,899/per year
Nordex Inc
Biotechnology
the United States
N
$120,416/per year
Nipro Corp
Biotechnology
the United States
E
$115,870/per year
Enovis
Biotechnology
the United States
A
$114,553/per year
Advanced Research Projects Agency - Energy
Biotechnology
the United States
M
$112,110/per year
MiniMed Inc
Biotechnology
the United States
L
$111,500/per year
Labcorp Drug Development
Biotechnology
the United States
L
$110,229/per year
Life Technologies Corp
Biotechnology
the United States
Z
$106,224/per year
Zimmer Biomet
Biotechnology
the United States
P
$103,077/per year
Promontory Therapeutics
Biotechnology
the United States
S
$102,181/per year
Steris PLC
Biotechnology
the United States
G
$97,274/per year
Gavin Conferences Pty Ltd
Biotechnology
the United States
E
$94,764/per year
Endeavor BioMedicines
Biotechnology
the United States
R
$94,402/per year
Replay Holdings LLC
Biotechnology
the United States
P
$94,235/per year
Pleno Inc
Biotechnology
the United States
S
$93,666/per year
Simulaids Inc
Biotechnology
the United States
N
$88,880/per year
NOIRLab/CAS
Biotechnology
the United States
O
$86,468/per year
Onward Technology
Biotechnology
the United States
L
$84,895/per year
LED Medical Diagnostics Inc
Biotechnology
the United States
E
$84,682/per year
Eyeco Ltd
Biotechnology
the United States
P
$84,523/per year
Paerosol
Biotechnology
the United States
I
$83,525/per year
IONIQ Sciences Inc
Biotechnology
the United States
S
$82,815/per year
Stateside PPE
Biotechnology
the United States
D
$82,041/per year
Digi Bio
Biotechnology
the United States
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FAQ about Clinical Programmer II
1. Where can a Clinical Programmer II earn the most?
A Clinical Programmer II's earning potential can vary widely depending on several factors, including location, industry, experience, education, and the specific employer.
According to the latest salary data by Salary.com, a Clinical Programmer II earns the most in San Jose, CA, where the annual salary of a Clinical Programmer II is $123,575.
2. What is the highest pay for Clinical Programmer II?
The highest pay for Clinical Programmer II is $113,600.
3. What is the lowest pay for Clinical Programmer II?
The lowest pay for Clinical Programmer II is $80,501.
4. What are the responsibilities of Clinical Programmer II?
Evaluates, develops, and maintains clinical database and analyzes clinical data. Codes, tests and documents databases. Performs data validation and develops algorithms for data management, typically using SAS programming language. May require a bachelor's degree. Typically reports to a supervisor or manager. Gains exposure to some of the complex tasks within the job function. Occasionally directed in several aspects of the work. Typically requires 2 to 4 years of related experience.
5. What industry pays the highest salary for Clinical Programmer II?
The Biotechnology industry offers the highest average compensation for Clinical Programmer II roles,
with salaries approximately 25% above the market median.
Where Does Our Salary Data Come From?
Salary.com provides salary estimates, histograms, trends, and comparisons using data from employer job postings and third-party sources.
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