The average custodian salary at San Diego was $50,468 , which is 31 percent lower than the average salary for this job in California, and 29 percent lower than the national average for this job . Custodian salaries at San Diego typically range from $24,537 to $71,034 (25th to 75th percentile). The highest reported custodian salary was $86,682. There are 39 employees at San Diego with the job title custodian.