The co-location was one of 49 approved by the Bloomberg administration that was reviewed by Mayor Bill de Blasio and Schools Chancellor Carmina Farina.
While nine plans were dropped by the review, both Staten Island co-locations, I.S. 49's and P.S. 16's, were given the go ahead.
The Eagle Academy/I.S. 49 co-location was criticized by parents and officials, some of whom were receptive of the program but not to it being co-located at the Stapleton school.
Sam Pirozzolo, president of the Staten Island's Community Education Council, who asked Farina to consider finding a different location for the Eagle Academy, said the school would take resources away from I.S. 49
"It's a mixed blessing," Pirozzolo said. ""The community and the neighborhood want the Eagle Academy very much. But we're hurting the existing program. We would like the Eagle Academy to have their own locations."
At a meeting in October, parents complained that an all-boys school would be put into the co-ed I.S. 49, and worried it would take over, according to the Staten Island Advance.
"They can't do this to these kids," Veronica Fitzgerald told the Advance. "These kids from Eagle Academy are going to take over. Students here already have to fight for everything they have."
With the plan approved, the DOE will initially put grades six to eight from the Eagle Academy inside I.S. 49, and eventually expand into high school.
Under the approved plan, a new elementary school will be moving in with P.S. 16. The DOE will reduce enrollment for P.S. 16 starting in September 2014.
Even with the DOE approving the co-locations, Pirozzolo said he was much more optimistic about the new administration. He said before the approvals went public, officials called him and let him know they were going through. Officials also told him they would eventually make changes to the decision-making process for co-locations.
"Moving forward the co-location will be significantly different than it is today," he said. "Council members will be notified much much longer in advance. I kind of was given the impression that maybe co-locations in the future will be much less frequent."