The 3-year-old boy who was found beaten in his Brooklyn home last week died on Sunday, police said.

Jaden Jordan had been in the hospital in critical condition for almost a week after he was found on Nov. 28 with a fractured skull and lacerations to his spleen and liver, law enforcement sources said. He also had a brain injury consistent with suffocation, strangulation or shaking, according to the criminal complaint.

His mother’s boyfriend, Salvatore Lucchesse, 24, who lives in the same home on West Fifth Street in Gravesend, was arrested and charged last week with assault and endangering the welfare of a child.

Charges against Lucchesse will likely be upgraded, a law enforcement source said.

Lucchesse told investigators that Jaden had fallen and hit his head when he put the boy in the shower after he allegedly defecated in his pants, law enforcement sources said. But police said Lucchesse’s story was not consistent with Jaden’s injuries.

The city’s Department of Investigation has begun an investigation into the events and the city’s Administration for Children’s Services’ handling of the case. ACS received an anonymous tip about Lucchesse the weekend before Jaden was found, but when it went to investigate, case workers learned the wrong address had been given. The agency said it did not receive the correct address before Jaden was found beaten.

Mayor Bill de Blasio said on Monday he is “very concerned” about Jordan’s death, but still has confidence in the leadership of ACS.

“Our job is to save every child, simple as that,” he said. “Sometimes we have the information that will give us the best chance to save a child, sometimes we don’t; but our job is to save every child.”

The mayor admitted that there’s still more to be learned about what happened to Jordan and ACS’ role leading up to his death.

“It’s clear that there was very focused action,” de Blasio said. “It’s also clear that this child died and my question is always going to be: Is there anything we missed, is there anything we could do better? That’s what this investigation will be about.”

De Blasio also pointed out that it’s less likely for people to hear the stories where ACS saved a life, “but in fact, many, many lives have been saved.”