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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 August 01, 2026, the average salary for a Clinical Programmer II in the United States is $97,990 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): $113,614
  • Majority Range (25th-75th percentile): $88,842 to $106,168
  • Entry-Level (10th percentile): $80,513
Salary Factors Salary-Boosting Skills Salary by Experience Related Job Salaries Top Paying Cities Explore Related Jobs

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 II 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): $72,191
  • Clinical Programmer II (2-4 years): $97,990
  • Clinical Programmer III (4-7 years): $107,709
  • Clinical Programmer IV (7+ years): $134,792
Job Role Years of Experience Average Salary
Clinical Programmer I0-2 years$72,191
Clinical Programmer II2-4 years$97,990
Clinical Programmer III4-7 years$107,709
Clinical Programmer IV7+ years$134,792
View as Graph

How Do Clinical Programmer IIs 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: $108,495.
  • California: $108,083.
  • Massachusetts: $106,643.

Top Paying Cities for Clinical Programmer II

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: $123,595
  • San Francisco: $122,242
  • Oakland: $119,665

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.
Skills Demand Percentage
Team Management 3.17%
Clinical Research 2.7%
SOP 2.22%
See More Skills

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 $118,568
21%
SOP $108,769
11%
Clinical Trial $107,789
10%
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 $110,132. While startup companies pay approximate $93,474.

Clinical Programmer II Salary by Company Size

Company Size Employees Average Salary
Startup 1~50 $93,474
Growth Stage 51~500 $98,774
Established 501~5000 $106,432
Enterprise 5000+ $110,132

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$122,488$59.025%
Healthcare$112,688$54.015%

How Education impacts an Clinical Programmer II's Salary?

Your level of education can impact your salary potential. While many Clinical Programmer II enter the field with a Bachelor's Degree, higher education can lead to more specialized and higher-paying roles.

According to our 100% employer-reported salary data, the median salary for an Clinical Programmer II with a Bachelor's Degree is between $84,533 and $89,751.

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%
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.

Last Updated on August 01, 2026
$88,842
Average $97,990/year
$106,168
$7,404
Average $8,166/month
$8,847
$1,709
Average $1,884/week
$2,042
$43
Average $47/hour
$51
Annual Salary Monthly Pay Weekly Pay Hourly Wage
75th Percentile $106,168 $8,847 $2,042 $51
Average $97,990 $8,166 $1,884 $47
25th Percentile $88,842 $7,404 $1,709 $43

Clinical Programmer II Salary Growth & Career Path

Clinical Programmer II

Next Role

Advancement

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.

Next Step Role Estimate Salary Projected Raise
EHR Certified Application Analyst III $120,550 23%
Clinical Programmer III $107,709 10%

Most common benefits for Clinical Programmer II

  • Social Security
  • 401 (k)
  • Disability
  • Healthcare
  • Pension
  • Time Off (days)

Common company salaries for Clinical Programmer II

Here are companies hiring for Clinical Programmer II and their salaries, click below for more details.

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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 $123,595.

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

The highest pay for Clinical Programmer II is $113,614.

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

The lowest pay for Clinical Programmer II is $80,513.

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.

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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