The average city clerk salary at San Diego was $231,664 , which is 29 percent higher than the average salary for this job in California, and 179 percent higher than the national average for this job . City Clerk salaries at San Diego typically range from $93,793 to $369,535 (25th to 75th percentile). The highest reported city clerk salary was $369,535. There are 2 employees at San Diego with the job title city clerk.