Semien grew up pitching and playing infield in El Cerrito Youth Baseball, across the bay from San Francisco, and was a member of the area’s All-Star teams. He went on to attend St. Mary’s College High School in Berkeley, California. At St. Mary’s, he hit .471 as a junior, .371 as a senior, and was named all-league three times where he was drafted by the Chicago White Sox in the 34th round of the 2008 MLB draft.
Semien chose not to sign and instead enrolled at the University of California, Berkeley, where he played college baseball for the California Golden Bears. After struggling as a freshman, Semien improved as a sophomore, hitting .328. As a junior, Semien was the starting shortstop for the team, but hit .275, hurting his stock for the MLB Draft.