He has previously played for the Montreal Expos/Washington Nationals, Arizona Diamondbacks, Milwaukee Brewers, New York Mets, and Los Angeles Dodgers.

He continued to pitch in the Marlins system through 2001 with the Kane County Cougars, Portland Sea Dogs and Calgary Cannons.

On July 11, 2002, he was traded by the Marlins (along with Wilton Guerrero, Cliff Floyd and cash) to the Montreal Expos for Donald Levinski, Justin Wayne, Carl Pavano, Mike Mordecai and Graeme Lloyd.

Vargas made his Major League debut on April 26, 2003, against the Houston Astros and recorded his first victory in a 6–3 win over the San Francisco Giants.

[2] In his Mets debut on May 14, 2008, he received a standing ovation from the Shea Stadium crowd, giving up only 2 earned runs and 3 hits, despite the loss to the Washington Nationals.

[3] He was expected to compete for a spot in the starting rotation during spring training, however, he suffered an arm injury and began the season on the 60-day disabled list.

Vargas pitched in middle relief for the Dodgers, until he was traded on July 31 to the Milwaukee Brewers for Minor League catcher Vinny Rottino.