Salary Range. Salaries for exercise physiologists vary by location, certification and experience. The median base salary is $42,264, with half of exercise physiologists earning between $37,479 and $48,431.hile just about anyone can call themselves a “personal trainer,” an exercise physiologist is a health care professional who has completed a degree in exercise physiology and/or has been certified by the American Society of Exercise Physiologists (ASEP).