The militant, who was holed up in a mosque since last night, was killed as he tried to escape, an army official said.
Security forces had launched an operation in Kanthpora village of Lolab following information about the presence of militants in the area.
“After a brief exchange of firing, at least one militant took shelter in a local mosque,” the official said.
The operation was on Thursday hampered by local residents who pelted stones at security forces.
Several policemen, including an officer, were hurt in the stone pelting, a police official said.
Kupwara is 85 kms from Srinagar.