The radio said the youth was seen being forced into a car in the Arab eastern half of the city.
His body was found several hours later in another part of the city, the radio said, describing it as a "suspected revenge attack."
Three Israeli teenagers were snatched from a road in the southern West Bank on June 12 and their bodies were found on Monday in a murder Israel has blamed on the Islamist Hamas movement.
Israel police said they were investigating reports of a kidnapping and confirmed finding a body but refused to say whether the two incidents were connected. They did not give details on the victim's identity.
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"In the early hours of Wednesday morning, police received a report of a person being forced into a car in Beit Hanina," police spokeswoman Luba Samri told AFP, referring to a well-heeled east Jerusalem neighbourhood.
"Within an hour, a body was found in Jerusalem that has still not been identified. We are looking to see if there is a connection between the two incidents."
Some time later, the family of the youth, who is understood to be around 16, reported him missing, it said.
Outside the home of the youth in Shuafat, which is very close to Beit Hanina, a large crowd of angry Palestinians were hurling stones at police, who were responding with sound bombs, an AFP correspondent said.
The body was discovered in a forest in Givat Shaul in southwest Jerusalem, the radio said. An AFP correspondent said police had sealed off a large area around the neighbourhood.