Abu Qasim was the most-wanted militant in Kashmir, which India and Pakistan claim in full but rule in part, said Syed Javaid Mujtaba Gillani, the chief of police in Indian occupied Kashmir.
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"It is a major success," Gillani said of the overnight security force operation centred on a village in the south of the Himalayan region.
Gillani said the killing of Qasim would dent the operational capabilities of LeT and hurt coordination between various militant groups. Qasim was a resident of Bahawalpur city in Pakistan, he said.
India has long accused Pakistan of pushing separatist militants into the held Kashmir to foment revolt in the Muslim-majority region. Pakistan denies those accusations.
Escalating tension over Kashmir led to the cancellation of a meeting between the national security advisers of the nuclear-armed neighbours in August.
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Pakistan last week committed to take "effective action" against LeT, which India also blames for an attack by suicide commandos on Mumbai in 2008 in which 166 people were killed. India welcomed the move.
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