The body of one of two boys who went missing together last weekend was pulled out of the Harlem River on Thursday, police said.

Garrett Warren, 13, of Harlem, and Alfa Barrie, 11, of The Bronx, were last seen together sometime between Friday afternoon and Saturday morning, according to cops.

Authorities recovered the body floating in the river near the Manhattan side of the Madison Avenue Bridge Thursday morning.

Cops believe it is the older child due the shoes found on the body, police sources said.

The city’s medical examiner will make an official identification and determine the cause of death.

“We’re taking it hard,” said a cousin of Garrett’s who answered his mother Dayshell Moore’s phone on Thursday afternoon and confirmed the body belongs to the boy.

Garrett was last seen in front of his home around 1:30 a.m. Saturday morning, cops said.

Surveillance footage obtained by police showed Garrett and Alfa walking together past a large group of people on Lenox Avenue around 6 p.m. Friday. 

Alfa was reported missing early Sunday morning and Garrett on Monday afternoon, Brian Gill, Deputy Chief Commanding Officer of Manhattan’s Detective Bureau, told reporters at a press conference on Tuesday.

“They both go to separate schools. We have them on video together leaving one of their residences and they were walking together at 145 Lennox when they were last seen” Gill said. 

The NYPD’s harbor unit has been scouring the nearby Harlem River for days.

“We’re going to search land, air and sea. Obviously the water is right here. They’re young children. We’re going to take every precaution. We have state of the art equipment, our helicopters. We have our harbor unit. We’re going to use all our assets to look for these kids,” Gill said. 

Alfa’s sister, 22-year-old Fatima Diallo, said her brother is the youngest of six and never doesn’t check in with his family.

“[His mom] has high blood pressure and he knows how she gets when her nerves are all, you know. So he’ll call just to say ‘mom I’m here you don’t need to worry,’ but he hasn’t done that,” she told The Post on Tuesday. 

Diallo said the family believed Alfa was at his older sister’s house, where he typically goes every Friday after school.

After talking to his friends, family members learned that Alfa had been hanging out with a kid who goes by the nickname of “Man man” and that child is Garrett, Diallo said. 

Diallo and her family had never heard of “man man” or Garrett before seeing his face on missing persons flyers, she said.

“I hope they find him. I really hope this is like them hiding. I just hope they’re both safe and okay,” she said. 

Garrett’s grandmother had told The Post that her grandson could usually be found playing basketball at Brigadier General Charles Young Playground. 

“One day. He’ll get mad and go to his fathers house but he’s never been gone this long and he would never miss Mother’s Day,” Candy Bojang said Tuesday. 

His mother had said it’s not like her son to go missing.

“He will maybe miss twenty or thirty minutes of his curfew but to be missing overnight? No. And also to not come home to eat? No,” Moore, 33, said Tuesday.

Additional reporting by Reuven Fenton and Craig McCarthy