Vargas decided to transfer out of LSU after the 2002 season to Cypress College for the season, picking a junior college so he would still be eligible for the draft. He was 11–3 with a 3.10 ERA and 101 strikeouts in 107.1 innings as he batted .374. He was the Southern California junior college player of the year for his work on the mound and at the plate. However, as the season wore on, his arm slot dropped, and his velocity fell into the mid-80s. That, combined with Vargas' signing bonus demands, depressed his draft stock, so he went undrafted.