Pérez graduated from Robinson School, a private, college-prep high school in San Juan, Puerto Rico. He went to Florida State University and majored in political science. He played college baseball under head coach Mike Martin for the Florida State Seminoles baseball team. In 1989, he played collegiate summer baseball with the Brewster Whitecaps of the Cape Cod Baseball League. As a Seminoles' junior in 1991, Pérez was named 2nd Team All-American by the American Baseball Coaches Association and 3rd Team All-American by "Baseball America", batting .370 with 11 home runs, 58 RBIs, and 30 stolen bases. That year, the Seminoles were also in the College World Series, and Pérez was a first-round draft pick (17th overall) of the California Angels.