Sources reported that the blast occurred soon after the Friday prayer at the mosque.
Jammu Kashmir Chief Minister Omar Abdullah, from his Twitter account, tweeted, "Maulana Showkat, head of the Jamat i Ahle Hadees has been killed in a blast in Srinagar. Will cool heads prevail? I pray they do."
The cause of the blast is yet to reveal, though the police suspected that the terrorists used an IED planted on a bicycle near the rear entrance of the mosque.
The religious leader Shokwat was injured at the explosion and succumbed to his injuries.