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Guidestar, a clearinghouse for information about nonprofits, has just published a new report on compensations at nonprofits that shows that female CEOs on average earn less than male CEOs, especially at the largest nonprofits.

In a sample available for free on Guidestar’s website, the report shows that for one category of 501(c)(4) organizations with budgets over five million dollars, male CEOs earned 38 percent more on average than female CEOs in 2009 ($465,547 versus $337,310) and at those organizations with budgets between one and five million dollars male CEOs earned 12 percent more than female CEOs ($149,391 verses $132,818).

On the other hand, at 501(c)(4) organizations with budgets between a half-million and one million dollars, male CEOs earned 9 percent less on average than female CEOs ($98,655 verses $107,594).

The report’s author, Chuck McLean, commented in a Chronicle of Philanthropy story that some of the gender pay gap in top jobs at the biggest nonprofits may be due to discrimination:

The size of an organization’s budget affects the compensation gap for a number of reasons, said Mr. McLean. “But probably the main reason is women have had such a difficult time getting into the larger organizations like colleges and universities, health-care institutions, and big-name nonprofits, so the penetration of women into those roles continues to go very slowly,” he said. “I think that there is still an old boys’ network out there.”

Claims about gender discrimination in compensation have long been subject to dispute—especially since Title VII of the 1964 Civil Rights Act made such discrimination of interest to the federal government (along with discrimination based on race, color, religion, and national origin).

One might think that there would be less discrimination in the world of nonprofit organizations, which are presumed to be less cutthroat than businesses and where the purpose of helping communities is more in line with the stereotype of women as nurturers. However, a 2008 story in Bloomberg Businessweek described a Corporate Library finding that the female CEOs earned 85 percent of what male CEOs earned—a gap much smaller than the gender gap in pay that Guidestar found at the largest 501(c)(4)s.

There is also a gender pay gap in the federal civil service. The General Accountability Office found in 2009 that even when it controlled for occupation, education, and experience, there remains 7 percent gender gap in compensation.

However, it’s not possible to conclude from all these reports of a gender pay gap that there remains widespread gender discrimination in top jobs.

As the Bloomberg Businessweek story and General Accountability Office report note, the findings of a gender pay gap do not account for all the possible reasons for the pay gap, such as a shorter average tenure for women in the CEO spot or varieties of experience brought to the job. Moreover, the Bloomberg Businessweek story notes that women may be less skillful at negotiating compensation packages that reward performance.

More women than in the past do occupy the top spot at large non-profits, including universities—such as University of Pennsylvania president Amy Gutmann and Barnard College president Debora Spar.

Still, the remaining gender pay gaps at nonprofits and in business and government do raise questions about whether Guidestar’s Chuck McLean is right that there remain ways in which women aren’t equally able to compete for the very top jobs and equally compensated when they do obtain those jobs. On that, the jury is still out.

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