The average Napa systems analyst salary was $158,438, which is 36 percent higher than the average salary for this job in California, and 112 percent higher then the average salary for this job nationwide. Systems Analyst salary in Napa is usually between $135,474 and $181,403 (25th and 75th). The highest systems analyst salary in Napa was $183,108. There are 4 employees in Napa whose job title is systems analyst.