Face coverings are required at airports, on PATH trains, and in the station, on AirTrains and bus terminals.
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Enforcement of the new rule began on Monday.
Anyone not wearing a mask will face a $50 fine.
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This move is part of the agency's commitment to supporting the New York and New Jersey state requirements on mask-wearing in transportation facilities.
The MTA began implementing its own mask fine back in September.
So far, police say they've only had to issue a handful of violations. They say it's to drive home the point that wearing a mask is mandatory.
And for travelers coming to New York from outside the Tri-State area, or Pennsylvania, there's a new testing requirement.
With cases surging in most states, the two-week quarantine rule is over.
Starting Wednesday, Governor Cuomo says travelers need a negative test within three days prior to landing in New York, followed by a three-day quarantine, and a negative test on day four.
"The fall is difficult for all of us. Globally, there are some countries that are closing down again so we expect an increase in the fall, but it's about managing the increase. That's what this is about," Cuomo said.
Essential workers are exempt from the quarantine rule, but everyone has to wear a mask.
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