The 16-year-old boy and the girl were apparently having an affair and wanted to get married which was rejected by their families.
The boy first shot the girl in the classroom while the assembly was taking place and then shot himself. It appears both had mutually agreed to die, police said.
The Gulshan-i-Fatima School is a well reputed private high school in the city's Patel Para area.
Police said a 9 mm pistol and two shells were recovered from the classroom besides the bodies.
The incident is being looked into from different angles and the families of both and the school people are being questioned, a police official said.
The police are investigating if and how the male student had managed to acquire a handgun and had brought it inside the school premises.
The suicide letters implored the parents to bury the two next to each other.
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