Ali Khail, a local government spokesman in Zabul Province, said Malim Abdul Habib was killed inside his house in the provincial capital Qalat on 3 January.
Habib was the headmaster of a high school attended by some 1,300 boys and girls.
The killing is the latest in a string of attacks on teachers and schools in the region. In October, gunmen shot dead a headmaster in front of his students at a boys school in Kandahar province.
Nabi Khushal, the director of education in Zabul Province, has blamed the Taliban for the killing, saying that "only the Taliban are against girls being educated."