Police shot Mudasir, accused of killing five-year-old Iman Fatima, in February 2017, saying he tried to escape.
However, a BBC Newsnight investigation has uncovered allegations that Iman's real killer is still at large.
DNA tests suggest Iman was killed by the same man suspected of murdering another child this month.
The rape and murder of six-year-old Zainab Ansari earlier this month sparked outrage and protests across Pakistan.
Police working on the investigation into Zainab's murder have discovered DNA traces matching those found in seven other attacks on young girls in the same city.
Out of the seven attack victims, four - including Iman - were murdered.
Until now, police and Iman's family thought her case had already been solved - but her family now believe the real killer is still on the run, while Mudasir was innocent.