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.