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:
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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.
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:
| 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 |
What Am I Worth?
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:
Demanded Skills for the Role:
| Skills | Demand Percentage |
|---|---|
| Team Management | 3.17% |
| Clinical Research | 2.7% |
| SOP | 2.22% |
| 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%
|
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.
| 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 |
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.
| Industry Sector | Average Annual Salary | Average Hourly Rate | Pay vs.Avg |
|---|---|---|---|
| Biotechnology | $122,468 | $59.0 | 25% |
| Healthcare | $112,670 | $54.0 | 15% |
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
| 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% |
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 July 01, 2026Promotions 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 | $120,549 | 23% |
| Clinical Programmer III | $107,701 | 10% |
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, .
| Year | Average Annual Salary |
|---|---|
| 2022 |
View More
|
| 2023 | $86,047 |
| 2024 | $86,257 |
| 2025 | $85,658 |
| 2026 |
View More
|
| 2027 |
View More
|
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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.
The highest pay for Clinical Programmer II is $113,600.
The lowest pay for Clinical Programmer II is $80,501.
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.
The Biotechnology industry offers the highest average compensation for Clinical Programmer II roles, with salaries approximately 25% above the market median.
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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