"He should still be in college. ... He needs more time to grow in so many areas, not just on the field but off the field," Kelly told SiriusXM NFL Radio on Monday.
Kelly said he recommended Kizer get more playing time at Notre Dame but added that he supported the quarterback's choice.
"Once a decision was made, we were united and we went to work to put him in the best situation," Kelly said.
When Kizer declared in December that he would enter the draft, ESPN draft analysts Mel Kiper Jr. and Todd McShay both said Kizer should have returned to Notre Dame for another season, though McShay listed Kizer as his No. 3 quarterback prospect last month.
Kizer started 23 games for the Fighting Irish, going 12-11. He threw for 5,809 yards with 47 touchdowns and 19 interceptions, adding 992 rushing yards and 18 scores on the ground.
Kelly touted Kizer as having the best skill set among NFL quarterback prospects, saying he would fit well if a team can draft him and give him time to develop.
"He's got a strong arm. Physically he's gifted," Kelly said. "He's got all those tools that you're looking for at the quarterback position."