The GM job had been vacant since Dec. 29, when the Jets fired John Idzik after two seasons.
"We interviewed a number of impressive, qualified candidates, but Mike Maccagnan clearly stood out," Jets owner Woody Johnson said in statement. "Mike’s attention to detail, strong personnel background, and collaborative approach to evaluating players made it clear that he is the right choice to be the next general manager of the New York Jets."
Johnson also credited longtime NFL executives Charlie Casserly and Ron Wolf for serving as consultants during the search.
Maccagnan spent the past 15 seasons with the Texans, working as director of college scouting for the past four seasons. He contributed to every draft in Texans history, bringing in All-Pro players such as wide receiver Andre Johnson and defensive ends Mario Williams and J.J. Watt.
Maccagnan also worked as a college scout for the Washington Redskins in 1994 and as a pro scout for the team from 1995-2000.
A Hightstown, N.J., native, Maccagnan was the only GM candidate who received a second interview with the Jets. The team interviewed seven candidates in total.
Maccagnan is tasked with hiring a head coach after the team fired Rex Ryan following six seasons and a 4-12 performance in 2014. The Jets interviewed Arizona Cardinals defensive coordinator Todd Bowles for a second time on Tuesday and Maccagnan was involved in the meeting, according to the Associated Press.
The Jets are also interested in Seattle Seahawks defensive coordinator Dan Quinn, who now must wait until next week to interview a second time since the Seahawks are still alive in the postseason.
"We have a solid foundation of players and a state-of-the-art facility in one of the most exciting and dynamic areas in America," Maccagnan said. "As with all teams, there are some areas we need to address, but we’re going to hire the right head coach, evaluate our personnel, and work together to build a football operation to get the New York Jets back on the winning track."
New York hasn't made the playoffs since 2010.
- Mike Fiammetta