You might think that a university CEO, given the responsibilities, would be the highest paid person in the institution.

At $492,650 for the 2014 fiscal year, Kansas University Chancellor Bernadette Gray-Little is the third-highest paid employee at the university, which is probably nothing to complain about. Yet in terms of how much Gray-Little is paid from state coffers, as opposed to funds from endowments or other sources, she ranks seventh at $221,692, according to figures released by the university.

Many administrators and faculty members throughout the university are paid from sources in addition to state funds – generally endowment funds. Those at KU who draw more from staff coffers than Gray-Little are: Doug Girod, executive vice chancellor of the KU Medical Center, $687,000; Garold Minns, dean of the Wichita medical school, $372,783; KU Provost Jeffrey Vitter, $368,480; Neeli Bendapudi, dean of the KU business school, $280,000; Gregory Unruh, KU associate professor in anesthesiology, $296,052; and Paul Terranova, vice chancellor for research at the KU medical center, $309,770.

Not many CEOs, given the chance to set the salaries of people they’re in charge of, would allow that to happen. But universities are different animals than private corporations and operate in a far different economic reality and organizational environment.

The KU chancellor’s salary, along with those of chief executives at all Kansas Board of Regents universities, is set by the Regents, while the chancellor determines the salaries of the various administrators and deans within the university. That means Gray-Little sets the salary for Doug Girod, the executive vice chancellor of the KU Medical Center, who gets paid $687,000, all of it from state funds, and is the highest-paid employee at KU.

Gray-Little, like university heads around the country, tries to compete in a job market in which a surgeon or physician or businessperson can make considerably more than the typical professional academic.

“It’s not unusual at universities for the head of an academic medical center to make more than the chancellor or president,” said Tim Caboni, KU’s vice chancellor for public affairs. “Someone who has opportunities outside (a university) is likely to be compensated according to those opportunities.”

Breeze Richardson, a spokeswoman for the Kansas Board of Regents, said that pay for the chancellor and other faculty is set to be competitive with their counterparts at similar institutions. “We’re paying the chancellor along the lines of what her peers are making,” she said. In the case of the top KU leader, peers would be those research universities that have medical centers and law schools as part of their system, Richardson said. Overall, the Gray-Little comes in at 86 on a list of university executive pay by the Chronicle of Higher Education.

Slightly less than half of Gray-Little’s paycheck comes from the state. The rest comes from private funds raised through the KU Endowment. In June of this year, the Regents announced raises in the pay of all its university CEOs, including Gray-Little, all of it through private funding and meant to keep their salaries competitive and keep the leaders in their positions, the Regents said at the time.

Endowed funds pay part or all of the salaries of many administrators and faculty members throughout the university. Complicating the pay picture further, many medical center faculty are also practicing clinicians and generate revenue from their practice.

Some of the highest paid employees at KU get paid relatively little from the state. Steven Stites, chair of internal medicine at the KU medical center and an endowed professor, makes only $25,853 in state funds, but his total salary is more than $400,000, the fifth highest at the university. Buddhadeb Dawn, director of cardiovascular diseases and an endowed professor as well, gets paid $14,376 from the state but makes $408,153 overall and is the fourth highest-paid employee at KU. John Sutphin, also an endowed professor at the medical center, receives no tax-funded salary at all but makes $360,060.