(United States). The average salary for a Physician Assistant (PA) in Boston, Massachusetts is $87,234 per year. The skills that increase pay for this job the most are Surgery and Critical Care.People in this job generally don't have more than 20 years' experience. Experience has a moderate effect on income for this job. Total Pay combines base annual salary or hourly wage, bonuses, profit sharing, tips, commissions, overtime pay and other forms of cash earnings, as applicable for this job. It does not include equity (stock) compensation, cash value of retirement benefits, or the value of other non-cash benefits (e.g. healthcare).