Clinical AI Engineer.
Madison.
$132,000
median salary, 9% below the national average
$100,000 to $169,000. Last updated April 2026.
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Data points to own the conversation.
The median Clinical AI Engineer salary in Madison is $132,000, 9% below the national average. Entry level starts near $100,000. Experienced professionals push past $169,000. Madison is a growing tech hub anchored by the University of Wisconsin and Epic Systems, one of the largest health IT companies. That spread is your negotiation window.
Salary range
Where do you fall?
Salary by experience
The gap between entry and lead level is typically $119,000. Where you land depends on years of experience and what you bring to the table.
Entry (0-2 yrs)
$86,000
to $106,000
Mid (3-5 yrs)
$112,000
to $139,000
Senior (6-9 yrs)
$145,000
to $172,000
Lead (10+ yrs)
$165,000
to $205,000
Salary trend
+6% YoYTotal compensation
Base salary is not the full picture. Equity, bonus, and signing can add $30,000 to the total package.
Base
$132,000
Equity
$16,000
Bonus
$11,000
Signing
$3,000
Estimated total: $162,000
How Madison compares
Madison, WI
$132,000
Cost of living: 5% below average
National Average
$145,000
Madison is $13,000 below
Clinical AI Engineer salary by city
Salary by role in Madison
What you should know
Before you negotiate a Clinical AI Engineer offer in Madison, understand the terrain. Madison is a growing tech hub anchored by the University of Wisconsin and Epic Systems, one of the largest health IT companies. The city consistently ranks among the best places to live and has a thriving startup ecosystem. Salaries are competitive relative to the modest cost of living. Compensation reflects the specialized intersection of ML engineering and clinical domain expertise. Engineers who can navigate FDA regulatory requirements, build AI systems for clinical decision support, and validate models against clinical outcomes earn premiums. Experience with medical imaging AI, EHR integration, or clinical NLP adds significant value.
Junior clinical AI engineers start at $100,000 to $115,000. Mid-level engineers building FDA-ready AI systems reach $135,000 to $165,000. Senior engineers leading clinical AI programs earn $170,000 to $210,000. Directors of clinical AI at hospital systems or health tech companies can reach $230,000 to $290,000 in total compensation. In Madison, cost of living sits near the national average, so the numbers you see are roughly what you keep.
Base salary is not the full picture. Equity at health AI startups adds $20,000 to $70,000 annually. Bonuses of 10% to 20% are standard. Benefits often include continuing medical education stipends and conference budgets. Some healthcare systems offer pension benefits and loan forgiveness programs. And on the tax side: wisconsin's top income tax rate is 7.65%. Madison has no city income tax. The moderate state rate is offset by the affordable cost of living and strong employer base. When someone quotes you $132,000, ask what the total package looks like. The gap between base and total comp is where real money hides.
On negotiation: Reference Epic Systems compensation benchmarks. Epic sets the salary standard for tech in Madison and most employers in the area compete against their packages. The range for Clinical AI Engineers in Madison runs from $100,000 to $169,000. That is not a narrow window. Where you land inside it depends almost entirely on whether you negotiate and how well you prepare.
Sources: SEC filings, H-1B LCA (DOL), BLS OES, 50+ job posting platforms. COL: BEA Regional Price Parities (2025). Data verified by Justin Bartak, Founder & Chief AI Officer. Last verified April 8, 2026. Full methodology
Considering a related role?
- A Conversational AI Designer in Madison earns $133,000 (1% more)
- The highest-paying role in Madison is Distinguished Engineer at $307,000
Common questions.
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