The minor Mardan girl was found dead in a sugarcane field in January.
The prime suspect, 15-year-old Muhammad Nabi, worked in a local restaurant and was also a close relative of the deceased.
He has confessed to his crimes, Inspector General (IG) Police Khyber Pakhtunkhwa Salahuddin Mehsud said today.
Addressing a press conference, Mehsud said during interrogation that the suspects confessed to trying to sexually molest the girl in the sugarcane field prior to strangling her to death.
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The IG claimed that it was a case of attempted rape before murder. However, a forensic report issued by the Punjab Forensic Science Agency (PFSA) had earlier confirmed that the girl was raped before she was murdered, it said.
Mardan Resident Police Officer Alam Shinwari claimed that the suspect had attempted to rape the child but ended up suffocating her to death with his hands after she began shouting and crying.
The other suspect has been identified as a close associate of the primary suspect. Police claim that Nabi had informed him about the killing.
Pakistan has seen a wave of protests in recent weeks over alleged police negligence.
The demonstrations were ignited by the rape and murder of a 7-year-old girl in the city of Kasur, whose body was found on a trash heap. Police have arrested an alleged serial killer believed to have killed her and seven other children.