Milton was a three-star dual-threat quarterback from Mililani High School in Mililani, Hawaii. He chose UCF because of new head coach Scott Frost, the former offensive coordinator of Heisman winning quarterback Marcus Mariota, whom Milton had idolized in high school. Milton started 10 games his freshman year leading the Knights to a 6–6 regular season record and an appearance in the Cure Bowl. The previous year, the Knights had gone 0–12. In his Sophomore year, Milton led the Knights to a 12–0 regular season record, winning the AAC and eventually the Peach Bowl against the SEC runner-up Auburn Tigers. Milton was named the AAC offensive player of the year. Milton placed 8th in the Heisman vote for 2017. Milton was named the offensive MVP in the 2018 Peach Bowl, despite not reaching a 50% completion rating (he had only been below 60% once for the entire 2017 year, and never below 50%), Milton threw for two touchdowns and went 13/18 in the second half. He ended the game 16 of 35 with 242 yards, 2 touchdowns and no interceptions. Milton also excelled with his legs, picking up 116 yards on the ground and scoring a touchdown, which led all UCF rushers. This was UCF’s first ever Peach Bowl win, and second New Years Six win in four years. Following the game, the school claimed a national championship.

On November 23, 2018, UCF played the last game of the regular season against in-state rival University of South Florida. Early in the second quarter, Milton pulled the ball on a belly option and ran right. He was tackled by two USF players with one player performing a clean hit with perfect form right below the knee. This caused Milton to dislocate his knee. He was carted off the field and then rushed to nearby Tampa General Hospital. Upon arrival, doctors found extensive damage to the arteries and nerves in his knee. Emergency surgery was undertaken to restore arterial blood flow. The surgery was successful. Two more surgeries followed over the course of several days. Milton was discharged from the hospital on November 30. Milton underwent reconstructive knee surgery in January 2019.