Born September 25, 1971, in Hinsdale, Illinois, John Terrence Lynch Jr. attended Torrey Pines High School in San Diego where he excelled in football, baseball, and basketball. Stanford University recruited him to play quarterback beginning in 1989, but after losing the starting competition entering his junior season, Lynch focused on pitching for Stanford's baseball team. The Florida Marlins drafted him in the second round (66th overall) of the 1992 Major League Baseball draft as a right-handed pitcher, and he threw the first pitch in the organization's history.