Kill, 52, had an epilepsy-related seizure last week -- his fifth since becoming the Minnesota football coach in 2011 -- and missed the Golden Gophers' game at Michigan.
Minnesota Director of Athletics Norwood Teague said Kill would take a leave of absence. Defensive coordinator Tracy Claeys will be acting head coach.
"Coach Kill is taking time to continue treatment and focus on managing his epilepsy," Teague said. "... Coach Kill will remain in very close contact with the team and his staff and provide direction and support as needed.
"Our support for Coach Kill is unwavering and we look forward to his return to full-time coaching duties."
Kill issued a statement thanking "everyone for their prayers and concerns."
"This was a difficult decision to make but the right decision," the coach said. "Every decision that will be made will be in the best interest of the players and the program. I look forward to returning to the Minnesota sideline on a full-time basis soon."
Kill is in his third season as the Golden Gophers' coach. His record at Minnesota is 13-18, including 4-2 this season. He has an overall coaching record of 140-91, which includes stints at Saginaw Valley State, Emporia State, Southern Illinois and Northern Illinois.