Certified Public Accountant (CPA) in Indianapolis Salary. The average salary for a Certified Public Accountant (CPA) in Indianapolis, Indiana is $60,366 per year. Experience has a moderate effect on income for this job. The highest paying skills associated with this job are Compliance (Financial), Tax Compliance, Financial Analysis, Tax Consulting, and Financial Reporting. $45,150 - $109,299. (Median)