He was called up to the Mets on May 13 after an injured Moisés Alou was sent to the disabled list, and took over the rotation spot previously held by Mike Pelfrey, who was optioned to New Orleans after posting an 0–5 record in 6 outings. His first outing as a Met was on May 17, a no decision in a 6–5 victory over the Chicago Cubs. His next outing as a Met was on July 3 against the Colorado Rockies. Vargas pitched 3.1 innings, giving up nine earned runs. He pitched only 10.1 innings for the Mets in 2007.