If a nonprofit's executive director salary is too high, your organization might face backlash, and if it's too low, you'll have trouble attracting top talent. According to Charity Navigator's survey of mid-to large-size nonprofits, the median salary of the average executive director was $147,273 in 2010.onprofit organizations use many formulas to set their chief executive's salary and compensation package, and making it a percent of the budget is among the most popular formulas. Additional considerations exist, especially in light of economic downturn, dwindling donations, organization size and other factors.