Payroll System Analyst Salary in San Diego, CA.
Updated on: Jan 14, 2026
How much does a Payroll System Analyst make in San Diego, CA?
The average Payroll System Analyst in San Diego, CA makes $122,951,
33% above the national average Payroll System Analyst salary of $92,140.
This pay is 12% greater than the combined average salaries of other metroes San Jose, CA, Las Vegas, NV, and Raleigh, NC.
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Payroll System Analyst Salary Average
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*Data is estimated and depends on the generous anonymous contributions of individuals