Jack Frew had been with a friend when they were assaulted in the Mossneuk area of the town on Thursday. The other boy was also injured.
Police said Jack’s body was found in a wooded area at about 1900 BST.
A spokesperson for the force said: “Jack had sustained a violent attack which caused his death. The motivation behind the attack is not yet clear.”
Detectives said they wanted to speak to anyone who was in the Mossneuk area in the early evening of Thursday.
In particular, they want to hear from anyone who saw or heard anything suspicious around the wooded area and cycle path near Wellsley Crescent and Mossneuk Road.
Pupils in Jack’s year at Duncanrig Secondary School have been told of his death and floral tributes and cards have been laid at the end of the pathway.
A statement posted on the school’s website before Jack’s name was released said: “Everyone at Duncanrig is shocked and saddened to hear of the death of a young man in East Kilbride last night.
“We are providing support for pupils at the school who have been very upset.”