Certified Auto Mechanic. Taking a vehicle to a certified mechanic for repairs is the most common method for replacing a fuel pump. The average cost of replacing a fuel pump is between $400 and $600 including parts and labor.This can vary depending on the make, model and year of the vehicle.ertified Auto Mechanic. Taking a vehicle to a certified mechanic for repairs is the most common method for replacing a fuel pump. The average cost of replacing a fuel pump is between $400 and $600 including parts and labor.