Police Commissioner Keechant Sewell and his parents had called on the public to help locate Conor Lian on Thursday.
He was last seen with his family near St. Patrick's Cathedral at the northwest corner of West 40th Street and Fifth Avenue when they became separated.
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He is from California and does not know the city, which prompted worry and concern.
The family said a group of protesters surrounded them and they lost sight of Conor.
NYPD launched a search Wednesday night, both in Manhattan and Flushing, Queens.
But by Thursday afternoon, officials say the boy found his way back to his relatives' neighborhood.
His parents thought it was unlikely he would be able to find his way back to his grandfather's house in Queens.
They said they wanted so badly to be searching for him but police told them to stay put -- and they are glad they did.
"Surprised, it was a miracle," his father, William Lian said.
He showed up on the front step of his grandfather's house while his parents were giving detectives information.
"He said he took the train, so I assume, we took the Long Island Rail Road to the city. He probably took the same route back," his mother Amy Lian said.
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The boy arrived back at the Laburnum Avenue home at around 3:05 p.m. He was taken to a nearby hospital to be checked out.
They don't know where he slept of if he ate, but his father said he looked OK.
They asked if he wanted something to eat.
"He said he's not hungry," the father said.
His parents have no idea how he knew how to get home but they are so grateful he did.
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"Everyone is so happy," he said.
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