Garcia joins on a free transfer after spending three years spent at Olimpia in his native country, the club previous signings Maynor Figueroa, Wilson Palacios and Hendry Thomas played for.
The 25-year-old becomes Owen Coyle's eighth signing of the summer transfer window and he was delighted the deal had been completed.
"Juan is a very talented player, a left-back, powerful and someone we're very happy to be bringing to the squad," he told the club's official website.
"He scored a tremendous goal for his country not too long ago so it's nice that he's got an attacking mind in his locker, but obviously he's coming in for his defensive abilities which will bring a lot to the group.
"Honduras internationals have a very good history at Wigan Athletic and we certainly hope he becomes another success story for us.
"It's an area of the team we're still looking to strengthen after a number of defensive departures at the end of last season, and we're leaving no stone unturned in doing so."
Garcia becomes the fifth Honduran to play for Wigan, joining Roger Espinoza at the DW Stadium, where he will wear the No 23 shirt.