The reopening came as fire officials revealed that "several" probationary firefighters have been hospitalized after contracting the disease — up from only one when the outbreak was first reported.
No new cases have been reported since last Wednesday.
FDNY Commissioner Daniel Nigro ordered the Randall's Island school to close on Friday and undergo a full cleaning focusing on high-risk areas including locker rooms, bathrooms and the auditorium, to help rid the place of the methicillin-resistant Staphylococcus aureus.
He also halted a training exercise that was causing knee wounds that spread the bug, according to the FDNY.
The number of confirmed cases of the superbug linked to the academy jumped to 13, up from 6, when it was first reported by DNAinfo earlier in August.
Possible and confirmed cases of probies with MRSA had also risen to 22 as the second training class in a row struggled with the stubborn germ.
It's not immediately clear if the impacted students would have to make up time or training at a future FDNY class, or if they could graduate on time.
There is an attendance requirement at the fire academy, but a source said that probies who got sick may be given extra time to make up the work.
A source said students would be working this week in the classroom doing Haz-Mat training and wouldn't be doing many drills.
MORE MRSA COVERAGE FROM DNAINFO NEW YORK
In addition to the massive scrubdown, students received a special antibacterial body wash, new work gloves, and extra T-shirts and shorts to wear during training, Gribbon said.
Their bunker gear was professionally cleaned and returned to them on Tuesday, with extra care taken to make sure the equipment remains fire-resistant.
Fans were also added to the room where the gear is stored to improve circulation.
The FDNY consulted with the Department of Health, an infectious disease specialist recommended by the DOH and the department’s own doctors to facilitate the cleaning.
The DOH referred all requests for comment to the Fire Department.
Medical officials would also continue to check for open wounds, since most cases of MRSA were spread by knees, according to the FDNY.
The kneee cuts were received during "Motivation Alley," a specific training exercise in which probies advance and operate hoselines, according to a memo sent last week by Nigro to every firehouse and EMT facility in the city.
The drill was halted until the Fire Academy obtains rubber mats, the memo said.
The FDNY said they began monitoring the MRSA cases in early August but took more drastic measures once the number of probies showing signs of infection doubled, according to Gribbon.
It's not the first instance of the superbug at the academy.
MRSA is usually spread by direct contact with wounds or contaminated hands or equipment, according to the Centers for Disease Control and Prevention.
It can cause pneumonia and bloodstream infections that could be life-threatening.