Malachi Flynn was born May 10, 1998 in Tacoma, Washington and is the son of Eric and Kristi Flynn. He has six older siblings. Flynn's sister, Angelica, competed in track and field at Washington State. Older brothers Isaiah and Josias also played college basketball. For high school, Malachi attended Bellarmine Prep, in Tacoma, where he compiled 1,625 career points, which ranked second in school history. After his senior season, Flynn won the Associated Press Washington Player of the Year award. For college, Flynn decided to attend Washington State, where he played basketball for two seasons. After his sophomore year, Flynn was named to the Pac-12 All-Academic Second Team with a 3.27 cumulative grade point average. He then transferred to San Diego State, where he had to sit out the 2018-19 season. In 2019-20, he earned Academic All-Mountain West honors and was named a Consensus Second Team All-American. At the close of his redshirt junior season, he declared himself eligible for the 2020 NBA Draft. Flynn initially attended Washington State for two years, from 2016 to 2018, before transferring to San Diego State. As a freshman at WSU, he scored 27 points on Nov. 30, 2016 in a win over Utah Valley. That season he started 30 of 31 games for the Cougars and posted 9.7 points, 2.9 boards and 2.9 assists per game. In his sophomore season at WSU, Flynn again started 30 games and improved his stats to 15.8 points, 4.3 assists and 3.4 rebounds per contest. But the team finished at 12-19 and Flynn decided to transfer to San Diego State, forcing him to sit out the 2018-19 season. As a redshirt junior at SDS, Flynn started all 32 games for the Aztecs and delivered 17.6 points, 5.1 assists and 4.5 boards per game. Flynn then earned Mountain West Player of the Year and Defensive Player of the Year honors and declared himself eligible for the 2020 NBA Draft.