The school spent another year dealing with off-field issues, from the eligibility of a top basketball player to a long-running academic scandal and now a reopened NCAA investigation. The Tar Heels also failed to win an Atlantic Coast Conference championship in any sport for the first time.
"We're wrestling with some of the toughest issues you can wrestle with," Cunningham said in an interview with The Associated Press. "It's taxing on the faculty. It's taxing on the faculty council. It's taxing on the coaches, on the students in the classroom. It is something that as an institution, we have to figure out how we can move forward."
UNC finished 14th in the 2013-14 Directors' Cup standings of the nation's top overall sports programs, the first time in six years and the fourth time in the competition's 21 seasons that it failed to make the top 10. Cunningham pointed to ACC expansion and parity as factors in the title-less season.
"It's not that the sky is falling," he said, "but you do need to pay attention and see what we can do to improve performance."
The highlight was women's tennis finishing as NCAA runner-up, while men's tennis reached the final eight, women's basketball came within a game of the Final Four and field hockey reached the national semifinals. Football -- led by Cunningham's first major hire, Larry Fedora -- regrouped from a 1-5 start to win a bowl game.
But much of Cunningham's third season was spent dealing concerns outside the lines.
The school spent much of 2013 investigating violations by NBA prospect P.J. Hairston before deciding not to seek his reinstatement from the NCAA, ending his college career.
Scrutiny of academics for athletes increased in January when a former UNC learning specialist told CNN that the majority of football and basketball players she studied from 2004-12 read at below-grade levels, though three outside researchers later said the data did not support her findings.
The school also hired former U.S. Justice Department official Kenneth Wainstein to investigate the causes of fraud -- first found in 2011 -- in the formerly named African and Afro-American (AFAM) department featuring classes with significant athlete enrollments and dating to the 1990s.
Then, in June, former basketball player Rashad McCants from the 2005 NCAA championship team told ESPN that tutors wrote papers for him and coach Roy Williams knew he took some of the AFAM classes in question. Weeks later, the NCAA said it was reopening its probe into academic misconduct because new information was available.
"It certainly has taken longer than I anticipated," Cunningham said. "In 2011 we all thought we had NCAA issues with agents and amateurism; 2012 is really when the academic challenges arose. In 2013 we had a chancellor leave ... so we've had a year of transition.
"It has been a long time to see similar issues arise. Now we're all hopeful that this final report that we're doing [from Wainstein] ... will bring closure to it."
Cunningham and provost James W. Dean Jr. have also spent the past year leading a review of how UNC handles academics for athletes, from the admissions process to academic support programs and NCAA compliance education. It will last into the fall.
Along the way, UNC has put some facility projects to the side while dealing with everything else.
UNC is looking at updates for an aging Fetzer Field, home to the soccer, lacrosse and outdoor track programs. UNC is also mulling upgrades or even a replacement to the Smith Center, the 21,750-seat home to men's basketball built in 1986. Both are still in planning stages.
"It's not always going to be perfect," Cunningham said. "I think what I have tried to bring to the department is a sense of calm, a sense of consistency that we are moving in a positive direction, that we do have a plan in how we can continue to improve and that we're working together for a common goal: for these students to have an outstanding experience."