Gunmen attacked Bhatti's car in a residential district of the Pakistani capital on Wednesday before fleeing.
He was dead on arrival at Islamabad's Shifa hospital.
Bhatti’s death comes two months after Salman Taseer, the governor of Punjab province, was assassinated by one of his police bodyguards.
Taseer had also campaigned against blasphemy laws and had publicly supported the cause of a Christian woman who was facing the death penalty for blasphemy.
Many religious leaders in the country supported the murder of Taseer.
Pakistan's law against blaspheming Islam carries the death penalty. No one has ever been executed for the crime, the law’s opponents say it is used to exploit personal enemies.