Benefits Specialist Salary. Benefits Specialist average salary is $48,680, median salary is $45,000 with a salary range from $33,030 to $75,000.Benefits Specialist salaries are collected from government agencies and companies. Each salary is associated with a real job position.enefits Specialist Salary. Benefits Specialist average salary is $48,680, median salary is $45,000 with a salary range from $33,030 to $75,000.