The average internal auditor salary at Fresno was $81,907 , which is 44 percent lower than the average salary for this job in California, but 9 percent higher than the national average for this job . Internal Auditor salaries at Fresno typically range from $81,872 to $81,941 (25th to 75th percentile). The highest reported internal auditor salary was $81,941. There are 2 employees at Fresno with the job title internal auditor.