Fedora compiled a record of 33-19 in four seasons at Southern Miss, including a school-record 11 wins this season. The Golden Eagles won the Conference USA title last week, upsetting then-undefeated Houston for the championship.
Before taking over at UNC, Fedora will guide Southern Miss in the Hawaii Bowl against Nevada on December 24.
"Larry has a strong record both as the head coach at Southern Miss and for 18 years as a college assistant coach," said North Carolina athletic director Bubba Cunningham. "Throughout his career, his teams have been known for their exciting and highly productive offenses and aggressive defenses."
Fedora's first team at Southern Miss broke 36 school records. He had previously been an assistant on the collegiate level at Oklahoma State, Florida, Middle Tennessee, Air Force and Baylor.
North Carolina finished 7-5 this season under interim coach Everett Withers, who will lead the Tar Heels in the Independence Bowl against Missouri on December 26.
"I especially want to thank Coach Withers, who did an outstanding job in leading the football program this year," Cunningham added. "Everett is an excellent football coach and a first-class individual. He and his staff provided exemplary leadership under trying circumstances and I am glad they were rewarded with an opportunity to play in a bowl game."