Beginning in 2003 as deputy athletics director at Army, Knowlton worked as a college athletics administrator. Knowlton later was athletics director at Rensselaer Polytechnic Institute from 2008 to 2015 and the U.S. Air Force Academy from 2015 to 2018.
From 2003 to 2006, Knowlton was deputy athletic director for the Army Black Knights athletic programs of his alma mater United States Military Academy.[6] Knowlton stepped down from that position in 2006 to direct the Center for Enhanced Performance on campus.[6]
On August 2, 2021, Knowlton announced that he had agreed to an eight year extension with Cal, keeping him in Berkeley through 2029.[16] Knowlton received the extension following his decision to give head football coach Justin Wilcox an extension through the 2023 season,[17] his decision to hire Mark Fox as head men's basketball coach,[18] and his decision to hire Charmin Smith as head women's basketball coach.[19]
In May 2022, Knowlton was cited as having been dismissive of complaints against Cal head women's swim coach Teri McKeever, who was accused by current and former Cal swimmers of bullying, verbal, and emotional abuse.[20] In June 2022, Knowlton received more pushback for telling current Cal swimmers and their families that the investigation into McKeever could take six months.[21] Knowlton responded to this pushback saying he shares the concerns of the swimmers and their families.[22]
McKeever was fired by Cal after an investigation that concluded in 2023.[23]
“I’m writing to inform you that today we have parted ways with long-time women’s swimming coach, Teri McKeever,” Cal athletic director Jim Knowlton wrote to Cal swimmers. “After carefully reviewing an extensive investigative report that was recently completed by an independent law firm, I strongly believe this is in the best interests of our student athletes, our swimming program, and Cal Athletics as a whole.
“The report details numerous violations of university policies that prohibit race, national origin, and disability discrimination. The report also details verbally abusive conduct that is antithetical to our most important values. I was disturbed by what I learned in the course of reading through the report’s 482 pages that substantiate far too many allegations of unacceptable behavior. I want to apologize, on behalf of Cal Athletics, to every student-athlete who was subject to this conduct in the past, and I want to thank everyone who had the courage to come forward and share their story with the investigators.” [24]
According to The East Bay Times/Southern California News Group, "But for dozens of current and former Cal swimmers, McKeever’s firing and the report did not go far enough. The weeks following the firing and release of the report have seen prominent financial donors to the university and its athletic program joining current and former Golden Bears swimmers and their parents in calling for the immediate dismissal of Knowlton and Simon-O’Neill, who critics allege ignored or failed to effectively address repeated credible allegations of bullying and harassment against McKeever."[25]
The East Bay Times/Southern California News Group also reported that UC Berkeley is taking additional steps beyond the firing of McKeever. UC Berkeley declined to comment on whether or not investigating Jim Knowlton and Jennifer Simon-O'Neill (Chief of Staff & Senior Woman Administrator) were part of those additional steps, but UC Berkeley assistant vice chancellor Dan Mogulof did confirm that as of this time, neither of the two have been placed on leave.[25]
On March 23, 2023, Scott Reid of the Southern California New Group reported that UC Berkeley has launched a formal investigation into Knowlton and Simon-O'Neill's handling of the allegations against McKeever.[26][27]
On March 29, 2023, Knowlton announced the hiring of Mark Madsen as the new head men's basketball coach at Cal. Madsen replaced Mark Fox, whom Knowlton hired four years earlier.[28]
On April 6, 2023, Nanette Asimov of The San Francisco Chronicle published an article[29] citing Knowlton as being dismissive of allegations of bullying against Cal women's soccer head coach Neil McGuire:
"Cal athletic director Jim Knowlton told one student’s mother — who also complained on behalf of her daughter — that a review found nothing to justify her allegations, according to an email from Knowlton reviewed by The Chronicle."
Asked whether UC Berkeley had properly investigated the claims, spokesperson Dan Mogulof said:
“When the current leadership of Cal Athletics is made aware of allegations that policies have been violated, or of complaints about employee behavior, they respond as a department, when appropriate, or refer the matter to appropriate campus investigative offices, when required."[29]