Pepe was selected by the Toronto Blue Jays in the MLB Draft. He was selected by the Blue Jays in the 31st round with the 924th pick overall. This past season as a senior, he hit .284 with six RBI. Earlier this season, he had a college career-high nine-game hitting streak. In two seasons with the Setters, Pepe batted .284 with 11 RBI and nine steals in 60 games.
Prior to joining Pace, Pepe played two years at Wagner College.