A manhunt was launched after the girl’s parents alleged he abducted her.
A senior police official told the BBC that the boy’s body also had injuries, though he gave no further details.
The extent of the 15-year-old victim’s injuries led many to draw comparisons with the 2012 gang rape and murder of a Delhi physiotherapy student.
Police had detained the boy’s parents for questioning following the discovery of the girl’s body on Saturday, but both of them have now been released, the official told BBC Hindi’s Manoj Dhaka.
Although it is unclear when the boy died, the PTI news agency said that the body had been in a “severely decomposed” state.
The case sparked outrage when details of the girl’s injuries became public.
Police had earlier said they believed the attack had been carried out by more than one person.
The incident, which was followed by the discovery of the body of another raped Dalit girl in another part of the state, has triggered protests against Haryana’s Chief Minister Manohar Lal Khattar.
Scrutiny of sexual violence has grown in India since the 2012 gang rape and murder of the 23-year-old student on a bus in the capital.
The crime sparked days of protests and forced the government to introduce tougher anti-rape laws, including the death penalty.
However, sexual attacks against women and children continue to be reported across the country. (Courtesy BBC)