Born in Gilroy, California, Jeff played college football at San Jose State University, and started his professional career as a backup to Doug Flutie with the Calgary Stampeders of the Canadian Football League. After Flutie was traded to the Toronto Argonauts Jeff Garcia took over as starting quarterback. He lead the Calgary Stampeders to a Grey Cup championship victory in November 1998, a game in which he was named the most valuable player.
Following the Grey Cup victory Jeff Garcia signed with the San Francisco 49ers of the National Football League. He set the 49ers' team record with 4278 passing yards in the 2000 season, although the team finished with a 6-10 record. Garcia led the 49ers to the playoffs in both the 2001 and 2002 seasons. He was named to the Pro Bowl in both of those seasons.