Johnsen was appointed the president of the University of Alaska system on July 28, 2015. As the system president, his priorities included a systemwide Title IX compliance effort, restructuring of academic programs and administrative services of the university aligning with Alaska's primary and secondary education sectors, and a systemwide push to achieve the State of Alaska's goal for 65 percent of Alaska's working age population to have a post-secondary degree or certificate of value by 2025.
Johnsen assumed the role of president during a period of budget cuts. The system had taken consecutive years of budget cuts as the state struggled with collapsed oil revenues. Johnsen made the case for supporting Alaska's higher education system, both extolling the virtues of education and the role the university can play in bolstering the state's economy. In July 2019, Johnsen presented possible structuring models for the university in the wake of declaration of financial exigency after 41% cuts to state funding. He said that "severe cuts were the only way to deal with the system's budget crisis".
Johnsen has faced votes of no confidence during his tenure, in 2017 and 2019, from both students and faculty across multiple universities. These votes of no confidence cited "a series of coercive and intimidating letters that UA President Jim Johnsen sent to the chancellors of UAA, UAF, and UAS," a letter of non-compliance with accreditation standards regarding clearly defined governance from the Northwest Commission on Colleges and Universities, and "a general trend of disregard for the wants and needs of the individual campuses in favor of President Johnsen’s plans."
Resignation
Johnson tendered his resignation amid blowback from a Wisconsin job search, among other reasons. Johnoson's resignation was accepted by the University of Alaska Board of Regents on June 22, 2020. He continued to be the president until July 1, 2020.
In June 2020, Johnsen was named the only named finalist in the University of Wisconsin system's presidential search. This is due in part to other applicants for this position withdrawing their names, fearing backlash for participating in this search during the COVID-19 pandemic. This led to criticism from UW faculty, students who called it a "Failed result of a flawed search process". On June 12 2020, Johnsen withdrew his name from consideration saying that the UW administration "have some important process issues to work out".