McRaven, 62, divulged in 2015 that he was diagnosed with leukemia five years earlier. He cited unspecified health concerns Friday as a factor in his surprise departure while stressing "they are not serious but they have caused me to rethink my future."
"There is going to be a lot of speculation as to why I am stepping down, but the fact is, this is a very personal decision for me," McRaven said during a regents meeting.
A University of Texas graduate and retired Navy admiral, McRaven had recent policy clashes with state lawmakers. His three-year contract expires at the end of the year.
McRaven had no professional academic experience when, in 2015, he was hired to lead the system of 14 campuses, 215,000 students and 90,000 employees. The chancellor's duties include representing the system in legislative matters, advocating higher education causes and fundraising.
McRaven plans to stay through the end of the current academic year in May, but mentioned entering the "fourth quarter of my life," saying "there are still a lot of things I want to do" including teaching, writing, traveling and "as, hackneyed as it sounds when someone is stepping down, I want to spend more time with my family.
"In the past 40 years, I have always put the job ahead of the family and I think it's time for that to change," McRaven said.
In a statement, the UT system said "McRaven has been public about chronic health issues over the past few years and a recent illness played a key role in his decision" but provided no further details.
McRaven was quoted in that statement as saying: "While I'm on the road to recovery and am grateful to my UT physicians and the good wishes and prayers of our many friends and colleagues, I believe it is time to segue to several other passions in my life."
Board of Regents Chairwoman Sara Martinez Tucker thanked McRaven at the meeting for "ensuring we have the best talent leading our institutions, driving inclusion and healthy campus climates."
McRaven's future appeared in doubt earlier this year after his decision to scuttle a controversial expansion project in Houston, as well as past clashes with state lawmakers over guns on campus and immigration policy. But, as recently as last week, the system said that McRaven would stay on as chancellor in 2018. He earns about $1.9 million annually.
The University of Texas System doesn't have an academic campus in Houston and McRaven's plan to build a data and research center surprised state and local officials, who said they weren't consulted. McRaven sparred with state lawmakers over the project at a tense legislative hearing, before announcing that he was ending the project and that any purchased land would be sold.
Earlier in his tenure, McRaven opposed an eventually successful state law allowing concealed handguns on campus, while advocating for preserving a law that allows immigrants in the country illegally to pay cheaper, in-state tuition. That policy has endured despite years of opposition from Republicans in the Legislature.
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