CharityWatch's "A+" to "F" letter grade ratings and financial efficiency ratios take into account how a nonprofit's employee salaries and other compensation are allocated among program, management & general, and fundraising functions.

Nonprofits generally allocate compensation based on how each member of staff spends their time. For example, the salary of a doctor who spends 100% of their time on a charity's program activities, such as providing direct medical care, would generally be allocated 100% to program. A fundraising or development executive's salary would be allocated 100% to fundraising. An executive director or president of a charity might spent 40% of their time on program activities, 25% of their time managing their nonprofit, and 35% on fundraising, and this person's compensation would be allocated among program, management & general, and fundraising expenses commensurately.

Due to differences in the way compensation is allocated by charities in their IRS Form(s) 990 and audited financial statements, high salaries do not necessarily indicate inefficiencies just as low salaries are not always beneficial. Rather than perceiving a particular nonprofit executive's compensation as too high or too low based on its nominal value, appropriate salaries are better determined by considering factors such as special skills needed for the position, relevant education and experience, and the complexity of a charity's operations. CharityWatch encourages donors to view each nonprofit's letter grade rating to better understand how efficiently it is operating overall prior to making a giving decision.