Raytheon Systems Salary. Raytheon Systems average salary is $71,341, median salary is $70,662 with a salary range from $44,800 to $93,028.Raytheon Systems salaries are collected from government agencies and companies. Each salary is associated with a real job position.aytheon Systems salary is full-time annual starting salary. Intern, contractor and hourly pay scale vary from regular exempt employee. Compensation depends on work experience, job location, bonus, benefits and other factors.