A woman is in custody after her 1-year-old son was smothered inside a midtown burger restaurant Monday afternoon, a law enforcement official with knowledge of the investigation said.

The woman was found inside the bathroom of the 5 Boro Burger restaurant on 36th Street, near Sixth Avenue, after an employee realized she had been in there for a long time. She was found with the toddler on her lap, foaming at the nose and mouth, police said.

The boy, who was not immediately identified, was taken to Bellevue Hospital Center where he was pronounced dead. His mother was taken into police custody, but had not been charged as of yesterday evening.

Marcus Comeau, 35, said he was standing down the block when he saw the mother being carted off by police and her son being wheeled out with a oxygen mask on his face.

“The mother was coming out in handcuffs,” he said. “She didn’t seem too distressed, kind of had her head down."

Employees jimmied the door open when others wanted to use the bathroom and couldn’t get in, police said.

The mother, who’s name wasn’t officially released by press time but was known around her Lower East Side apartment as “Honey,” was also widely known to have mental health issues.

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“One day she’d say ‘hi’ to you, one day she doesn't," said Rafael Brenes, 53, adding he would often see the baby with his father. “It seemed like a happy baby. The baby was well taken care of.”

The woman had a reputation of being volatile. Neighbors spoke about a violent incident years ago involving her and her family.

“She’s had problems in the past,” said Carolyn Lawson, 47, who also lives in the building. “It’s really sad, I don’t understand it."