WASHINGTON — The Air Force secretary, Heather A. Wilson, said on Friday that she would resign after two years of reining in Trump administration plans for a widely criticized Space Force and overseeing a branch of the military that is involved in lengthy air campaigns over Afghanistan, Iraq and Syria.

Ms. Wilson, one of the highest-ranking women at the Pentagon, had been considered a potential successor to Jim Mattis, who stepped down as defense secretary in December. Instead, she announced in a resignation letter that she would become president at the University of Texas at El Paso, after a vote by the university’s Board of Regents.

She plans to remain at the helm of the Air Force until May 31, allowing time for a “smooth transition,” she wrote in the resignation letter, which was first reported by Reuters.

“American higher education needs strong leaders to meet the challenges of the 21st century,” she wrote. “It has been a privilege to serve alongside our airmen over the last two years and I am proud of the progress we have made restoring our nation’s defense.”

Her departure clears one hurdle for the elevation of Patrick M. Shanahan, the acting defense secretary, to the Pentagon’s top job. Defense Department officials said Ms. Wilson had a tense relationship with Mr. Shanahan, who is unwavering in his vocal support of President Trump — including of plans for a Space Force.

Several Defense Department officials said that they expected the president to formally nominate Mr. Shanahan as defense secretary, but the president has been known to change his mind.

Ms. Wilson successfully worked to ensure that a newly created Space Force would be part of the Air Force instead of becoming a separate military branch, as Trump administration officials had initially planned. She also argued that creating the Space Force would be expensive and build a new bureaucracy that would risk slowing space development, just as the United States confronts fresh challenges in the field.

Mr. Shanahan had helped push a Space Force independent of the Air Force.

Additionally, in September, Ms. Wilson announced the Air Force’s aim to increase its number of squadrons to 386 by 2030, from 312, anticipating a great power conflict with Russia and China.

The pivot to future wars came as Ms. Wilson was already grappling with shortages in readiness — including wear and abuse on the Air Force’s fleet of aircraft — for missions in Iraq, Afghanistan and Syria. In October, Mr. Mattis ordered the Air Force to increase mission capable rates for some squadrons, to 80 percent by the end of 2019 from roughly 70 percent.

A Rhodes Scholar, Ms. Wilson was one of Mr. Trump’s first appointees at the Pentagon, for which she left her job as the first female president of the South Dakota School of Mines and Technology.

Mr. Trump said that Ms. Wilson “has done an absolutely fantastic job” and congratulated her selection as president of the El Paso campus at the University of Texas, which he said was effective Sept. 1.

Helene Cooper contributed reporting.

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