The average San Diego city clerk salary was $231,664, which is 29 percent higher than the average salary for this job in California, and 179 percent higher then the average salary for this job nationwide. City Clerk salary in San Diego is usually between $93,793 and $369,535 (25th and 75th). The highest city clerk salary in San Diego was $369,535. There are 2 employees in San Diego whose job title is city clerk.