[4] Jenkins earned bachelor's and master's degrees in philosophy from the University of Notre Dame in 1976 and 1978, respectively, and was ordained a priest of the Congregation of Holy Cross in the Basilica of the Sacred Heart on campus in 1983.

[11][12] Early in his tenure at Notre Dame, Jenkins was criticized for other decisions such as allowing performances of The Vagina Monologues and showings of gay films on campus.

[13] Jenkins' decision to include an invitation to President Barack Obama to deliver the 2009 commencement address at Notre Dame and to receive an honorary degree was controversial.

[15] In 2016, Kevin C. Rhoades, the bishop of Fort Wayne-South Bend, said that he disagreed with Notre Dame's decision to honor Vice President Joe Biden and John Boehner, the former speaker of the U.S. House of Representatives, with the university's Laetare Medal; Rhoades said he would have preferred the university to invite Biden and Boehner to speak "rather than bestow an honor that can provoke scandal.

[20] On September 26, 2020, Jenkins attended the White House Supreme Court nomination ceremony for Notre Dame professor judge Amy Coney Barrett.

Days before the diagnosis, after photos were published, Jenkins publicly apologized for not wearing a mask nor adhering to social distancing guidelines.

[22] Jenkins was also criticized by the faculty for not following the strict health policy he imposed on campus while in Washington, for traveling while he has forbidden them and students to, and for opening Notre Dame's reputation to political exploitation.

[22][23] A student-authored petition that called upon Jenkins to resign gathered 213 signatures—a number equal to approximately 2.5% of the size of Notre Dame's undergraduate student body.