A 4-year-old boy became separated from his mother at a busy Brooklyn subway station during the Tuesday morning rush hour, and wound up all the way in lower Manhattan — but is safely back at home thanks to a good Samaritan and the NYPD, cops said.

Messiah Cummings was walking with his mom through the massive Broadway Junction station in East New York around 8:00 a.m. when he and his mom lost sight of each other, officials said.

“I was screaming, crying, looking for him,” Messiah’s “panicked” mom, whose name wasn’t released, told NBC 4 – New York. “I thought someone took him.”

Instead, the intrepid tot ambled onto a Manhattan-bound J train, while cops who’d met up with his frantic mom emailed a photo of Messiah to every cop in the department, and tweeted out the same picture to the public.

As the train rumbled over the Williamsburg Bridge and into the Lower East Side, one fellow rider recognized the pint-sized straphanger from online alerts, police sources said.

The good Samaritan, whose name wasn’t released, brought Messiah to his office on the Bowery, called the police, and fed him breakfast while they waited.

“We went to the kid to make sure that he’s healthy, not scared, in good shape,” said Officer Chester Chung, who along with his partner went to pick up the wayward tyke. “I asked him a couple of questions. Very intelligent kid.”

“He said he was lost, and walked away from his mom, and the guy brought him to his workplace,” Chung said. “We made sure that he wasn’t hungry, bought him a Happy Meal. … He wanted his toy.”

The cops brought Messiah back to their station house, where they snapped a photo of him grinning and doodling in an NYPD coloring book.

They also put Messiah and his relieved mom in touch over Facetime, before she arrived for a joyous reunion.

She “was overwhelmed and excited that she had found her child,” said Chung’s partner, Kevin McArdle. “I was thrilled that it was the kid, that we found him, that he wasn’t harmed, that we were able to reunite [him with] his mother.”

Messiah was just as happy to be home.

“I missed my mommy,” the tot told NBC.

Added his mom, “I’m stressed. But I’m happy he’s OK.”

Additional reporting by Ben Feuerherd