According to the AAMA 2011 Medical Assisting Salary Survey, average gross salary for certified medical assistants (CMAs) is $29,460. This is a national average, so it might be more or less depending on your area. The average gross pay for non-certified medical assistants is $26,568.here is sometimes a $10,000 difference between a beginning certified medical assistant and a CMA with 16+ years experience. The best type of medical facility for higher pay (based on years of experience) is in a Emergency and outpatient hospital department or medical and surgical specialties..