The suspect is being interrogated in the killing of the child whose body was found at an isolated place near Khedli village near Aligarh town on Sunday morning, Aligarh police station SHO Ram Krishan said.
Condemning the incident, Chief Minister Ashok Gehlot said on Sunday night that the accused will not be spared.
"The rape and murder of the minor girl is highly condemnable and shameful. The accused of the heinous crime will not be spared," Gehlot said.
Police said the suspect was caught on the basis of evidence collected from the crime scene.
The child went missing after a sports function in school on Saturday. The function got over at 3 pm and she was not seen after that.
Her family members started looking for her and found the body the next morning in an isolated spot about 400 metres from the school.
She was strangled to death with her school belt which was tied around her neck.
Six-year-old girl raped and murdered in Rajasthan's Tonk; police detain 40-yr-old, accused won't be spared, vows Ashok Gehlot