WACO, Texas—Baylor University regents on Thursday fired the school president, the second in three years to leave amid clashes with the faculty at the world’s largest Baptist university.

Board Chairman Howard K. Batson repeatedly declined to discuss why John M. Lilley was fired, referring instead to the board’s lack of “confidence in John’s ability to unite various Baylor constituencies.”

The action came during the regents’ annual summer retreat, held this year in the Dallas suburb of Grapevine.

“Perhaps progress wasn’t as swift as far as some of us would hope as far as bringing the Baylor family together,” Batson said Thursday on a conference call. “We need a new president who will listen to all the divergent voices in the Baylor family.”

Lilley was hired in November 2005 after regents’ unanimous vote, five months after embattled President Robert Sloan stepped down and became the school’s chancellor in a deal worked out with regents.

Sloan, who had been president since 1995, had been blamed for rising tuition costs and rifts among professors who had been calling for his ouster for months.

In a statement Thursday, Lilley said he accepted the Baylor post aiming to help “heal the wounded hearts left in the wake of the conflict that preceded us,” but it became clear immediately that regents reflected “some of the deepest divisions in the Baylor family.” He said he was proud of the work he had done as president to bring the university together and help it achieve its goals.

“I deeply regret the action of the board, and I do not believe that it reflects the best interests of Baylor University,” Lilley, a Baylor alumnus, said in the statement.

In May, the faculty senate passed a resolution critical of Lilley, focusing mainly on concerns that professors did not have input on decisions to grant tenure.

But last month Lilley held a summit with faculty and administrators to review and try to improve the tenure process, and professors were still looking at the recommendations.

Dianna Vitanza, a faculty senate member, said the summit went “very well.” She said she was not completely surprised by Lilley’s firing but declined to speculate on the reasons for the regents’ decision.