The 18-year-old forward led his club with 13 goals and added three assists in 31 games, including 24 starts.
Pepi received 39.47% of the votes from MLS players, technical staff and media members. Revolution midfielder Tajon Buchanan was the runner-up at 31.1%.
Pepi has produced 15 goals and four assists in 55 matches (28 starts) since making his MLS debut in 2019.
He also made his debut earlier this year with the United States men's national team. In six appearances, he has three goals.
The Young Player of the Year award honors the top player in the league age 22 and under. Players born on or before Jan. 1, 1999 were eligible for selection.