Imran Ali, 24, pleaded not guilty to the offences against six-year-old Zainab Fatima Ameen in the Punjab city of Kasur last month, said defence lawyer Mehr Shakeel Multani.
"The police have levelled baseless and false allegations against my client," Multani told AFP.
The hearing was held in Lahore's Kot Lakhpat prison for security reasons. Witnesses will be called on Tuesday.
Zainab's murder last month sparked outrage across Pakistan, with riots erupting in Kasur as thousands swarmed police stations and set fire to politicians' homes, while Pakistanis took to social media demanding action.
At least four other cases of rape and murder have been recorded in the Kasur area in the past two years, but it is not yet clear if they are linked.
According to the victim's father Ameen Ansari, Ali -- who lived nearby -- had taken part in the initial protests that erupted after Zainab's body was discovered.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)