Highest Jefferson City employee salary in year 2016 was $192,960. Jefferson City employees number in year 2016 was 45. Jefferson City average salary was $43,108 and median salary was $28,650. According to the last payroll, Jefferson City average salary is 42 percent lower than USA average and 11 percent lower than Missouri state average. Jefferson City employee salaries are usually between $15,506 and $59,153. Top 10% of highest-earning employees have salaries ranging from $123,160 to $192,960.