The move comes amid increased demand at local stations along the line and decreased ridership at the express stations.
Under the plan, trains will stop at Prince Street, 8th St-NYU, 23rd Street, 28th Street and 49th Street from midnight to 6:30 a.m., stations which are covered by the N trains, according to the agency.
Currently the Q stops at Canal, 14th, 34th, 42nd and 57th streets. The R, which runs along the line does not have late night service.
Riders at local stations will see their travel times reduced by more than five minutes and riders at express stops will see their travel times increased by about one minute, the MTA added.
“We are constantly analyzing service and ridership trends in order to provide the best service possible to all of our customers at all hours,” NYC Transit President Carmen Bianco said in a statement. “As we saw increased ridership at local stations along the Broadway Line, it simply made sense to provide these customers with more service.”
The service change will primarily benefit riders going to or from a local station in Manhattan to another point in the borough and will cut the current average wait time of 10 minutes in half, according to the MTA.
MetroCard entries increased 28 percent at local stations in Manhattan from 2008 to 2012, the agency said, and decreased at express stations by 12 percent during the same time period.
Riders traveling to Brooklyn may see increased travel times but would not have to walk to an express station to catch a Q train.
Riders heading to Queens will not be impacted because the Q terminates at 57th Street in the overnight hours, an MTA spokesman said.
The change does not need to be approved by the MTA board and will cost $73,000 each year, according to the agency.