Abu Khedair was heading from his home to a mosque in the middle-class neighborhood of Shuafat for prayers around 4 a.m. Wednesday when three men forced him into a car and drove off, his father, Hussain Abu Khedair, said.
The boy's body was found about an hour later in a forest in West Jerusalem.
Israeli police have said they are looking into the possibility that his death was related to a family dispute as well as the alternative theory that it was a revenge killing.
"The investigation is continuing. We are still looking at the possibility to determine if we are talking about a criminal incident or a nationalistic incident," Israeli police spokesman Mickey Rosenfeld said.
Arrests after Israelis kidnapped
Since the June 13 abduction of the Israeli teens -- Eyal Yifrach, Gilad Shaar and Naftali Frankel -- on their way home from school, Israel has arrested hundreds of activists from Hamas, the militant Islamic organization it blames for the kidnapping.
Israeli forces have also destroyed the homes of the two main suspects it has identified in the Israeli teenagers' abduction.
WAFA, the Palestinian state news agency, reported Wednesday that 15 Palestinians have been killed during that time. The figure includes six killed by Israeli troops in the West Bank, three in an Israeli airstrike in Gaza, two dead of heart attacks after West Bank raids, plus the recently slain Palestinian teenager.
Hamas has praised the kidnappings of the Israelis but denied that it was responsible for what happened. It warned that if Netanyahu "brings a war on Gaza, the gates of hell will open to him."
This week's unrest comes as Israelis and Palestinians continue to trade blows over longstanding issues. There have been rocket attacks and airstrikes.
The IDF said 40 rockets were launched toward Israel from Gaza on Thursday. One soldier had minor wounds and some homes were damaged, the IDF said.
Israel conducted at least eight airstrikes early Thursday.
Three hit a Hamas intelligence building in Gaza City, while at least one struck a Qassam training camp in Beit Hanoun.
Palestinian medical sources reported at least 10 people injured, one of them seriously.
The IDF said the airstrikes, aimed at 15 Hamas targets, were in response to the firing of more than 20 rockets into Israel since Wednesday.