Functional Analyst Salary. Functional Analyst average salary is $68,774, median salary is $65,000 with a salary range from $36,150 to $145,600.Functional Analyst salaries are collected from government agencies and companies. Each salary is associated with a real job position.Functional Analyst salary statistics is not exclusive and is for reference only. They are presented as is and updated regularly.unctional Analyst salaries are collected from government agencies and companies. Each salary is associated with a real job position. Functional Analyst salary statistics is not exclusive and is for reference only. They are presented as is and updated regularly.