New Yorkers are being warned to brace for intense thunderstorms and flash flooding come Thursday afternoon — with as much as 5 inches of rain expected in just a matter of hours as commuters battle the evening rush hour.

The National Weather Service predicted up to 3 inches per hour across parts of the city — as forecasters warned the worst soaking will be felt between 5 p.m. to 6 p.m. just as people attempt to trek home.

“It’ll definitely impact the evening commute in the form of thunderstorms,” Fox Meteorologist Stephanie van Oppen told The Post.

The NWS forecasted up to 5 inches of rainfall in some areas with the majority of that deluge falling between in as little as 3 to 6 hours Thursday afternoon and evening.

The sudden alerts were blasted out as sunny, near-cloudless skies still lingered over the Big Apple.

Still, the city’s emergency management agency urged people to avoid travel over the next 24 hours.

The threats of commuter chaos came after the city’s subway system was already plagued by morning delays due to a possible heat-related power outage at Manhattan’s West 4^th Street station, the second time this week. 

Residents whose homes frequently flood were also being cautioned to prepare to flee if the conditions worsened quickly.

The “severe flooding” was forecast across the city and parts of Long Island – with the NWS blasting out a flood watch for the region from Thursday at 2 p.m. through Friday 8 a.m.

A state of emergency was declared over in New Jersey as the Garden State braced for severe flooding and as much as 7 inches of rain.

“This storm system could bring intense rainfall rates and amounts in a very short period of time,” New York City Emergency Management Commissioner Zach Iscol said.

“Every New Yorker should always be prepared for dangerous weather. Make a plan now, stay alert to changing conditions, and be ready to move quickly at the first sign of rising water, especially if you live in a basement or other below-grade space.”

“Flash flooding is one of the most dangerous hazards we face in New York City because it can happen quickly and without warning,” Mayor Eric Adams said.

“Our emergency teams and city agencies are fully mobilized and prepared, but New Yorkers must also take steps to stay safe,” he added.

“Sign up for Notify NYC, know your exits if you live in a basement apartment, and be ready to act before conditions become life-threatening.”

Meanwhile, New Jersey’s state of emergency went into effect at 2 p.m.

“Beginning this afternoon, we are expecting severe thunderstorms to bring heavy rainfall and damaging wind gusts with the potential for flash flooding across the state,” Lt. Gov. Tahesha Way said. 

“I urge all New Jerseyans to remain alert, follow all safety protocols, and monitor the proper channels for the duration of these storms. Residents should remain off the roads and indoors unless absolutely necessary.”