The girl was kidnapped from her neighbourhood on January 4. She was raped and later murdered. Her body was found from a heap trash on January 9.
Investigators found an empty box near the body of the girl and one of the suspects arrested on Friday was identified by the help of a forensic examination, Dawn News on Saturday quoted unnamed sources as saying.
Six rape cases were already registered against the suspect. The other suspect is his brother and similar cases are registered against him.
Sources said the two brothers were residents of the College Road area in Punjab province where a minor rape survivor was found in November. The girl is still under treatment at Children's Hospital, Lahore.
The joint investigation team formed on January 10 to probe the rape and murder case has collected data of 300 mobile phone numbers and six of them have been marked for further investigation.
Sources said locator vans had been working in Punjab's Kasur city for the past three days to trace the location of the two suspects.
They said they were arrested from a place outside the district where they were hiding. Police had interrogated around 1,300 people and released many of them after their DNA tests.
Also on Friday, Punjab Inspector General of Police Arif Nawaz said that investigators were going in the right direction.
A new video footage emerged on social media regarding a suspect moving near the house of the victim.
A police official said that the JIT had not released any video footage. In fact, the video clip was the initial part of the first video shared by the family of the victim with the JIT.
Separately, on a call at helpline, police raided two rented houses in Ali Park and Peerowala Road whose tenants had gone missing. Police took the owners into custody to know the whereabouts of the tenants.
Pakistan's National Assembly Speaker Sardar Ayaz Sadiq on Friday formed a 10-member committee for suggesting recommendations to stop child abuse incidents.
The committee has been asked to give its recommendations to the house within 30 days.