The average annual salary for the CEO of a nonprofit organization is $102,000, as of 2015, according to PayScale. However, the salary can vary based on factors such as location and experience level. The budget of the nonprofit can also affect a CEO's annual salary.
A CEO of a nonprofit organization may also receive compensation in the form of bonuses and profit sharing, which can increase annual earnings. Additional non-monetary benefits, such as a flexible work schedule, paid travel to company or industry events, or employer-paid benefits, may also be a part of the total compensation package for a nonprofit CEO.