The 26-year-old Pagan goes to the Mets in exchange for two minor-leaguers.
Pagan was drafted by the Mets in 1999 and traded to the Cubs in 2006. He hit .264 with four home runs in 71 games last season.
In exchange for Pagan, the Cubs got pitcher Ryan Meyers and outfielder Corey Coles.
Meyers was 1-4 as a relief pitcher for two Class A clubs last season. Coles batted a combined .286 for three teams.