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Clinical Programmer II Salary in the United States

How much does a Clinical Programmer II make in the United States?

As of March 01, 2026, the average salary for a Clinical Programmer II in the United States is $97,916 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): $113,503
  • Majority Range (25th-75th percentile): $88,766 to $106,075
  • Entry-Level (10th percentile): $80,435
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View as table View as graph 25% $88,766 10% $80,435 90% $113,503 75% $106,075 $97,916 50%(Median) Didn’t find job title? Click

Clinical Programmer II Salaries by Percentile

Annual
Salary
Monthly
Pay
Weekly
Pay
Hourly
Wage
75th Percentile $106,075 $8,840 $2,040 $51
Average $97,916 $8,160 $1,883 $47
25th Percentile $88,766 $7,397 $1,707 $43
Check out Clinical Programmer II Job Openings in the United States
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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): $72,158
  • Clinical Programmer II (2-4 years): $97,916
  • Clinical Programmer III (4-7 years): $107,670
  • Clinical Programmer IV (7+ years): $134,720
Job Role Years of Experience Average Salary
Clinical Programmer I0-2 years$72,158
Clinical Programmer II2-4 years$97,916
Clinical Programmer III4-7 years$107,670
Clinical Programmer IV7+ years$134,720
$72,158 Clinical ...
$97,916 Clinical ...
$107,670 Clinical ...
$134,720 Clinical ...
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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: $108,413.
  • California: $108,001.
  • Massachusetts: $106,562.

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: $123,501
  • San Francisco: $122,287
  • Oakland: $119,575

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
$118,478
21%
SOP
$108,687
11%
Clinical Trial
$107,708
10%
Team Management
$106,728
9%
Innovation
$105,749
8%
Project Management
$105,749
8%
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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
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%
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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.

Last Updated on March 01, 2026

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 $120,547 23%
Clinical Programmer III $107,670 10%

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.

Find Your Next Clinical Programmer II Job

Ready to take the next step in your career? Browse thousands of current Clinical Programmer II job openings on our job board. Use the search bar below to find your perfect match.

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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 $123,501.

2. What is the highest pay for Clinical Programmer II?

The highest pay for Clinical Programmer II is $113,503.

3. What is the lowest pay for Clinical Programmer II?

The lowest pay for Clinical Programmer II is $80,435.

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.

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.

We offer detailed salary information across multiple percentiles for your reference. (Click here to learn Why the Salary Midpoint Formula Is Crucial for Achieving Pay Equity.)

With the most extensive online, real-time compensation data available, Salary.com helps you pinpoint your exact pay target.

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