Demonstrations broke out in several parts of Kashmir, particularly in Shia-majority areas, following reports that Khamenei was killed in a US-Israel strike.
Omar Abdullah appealed to all communities to maintain peace and avoid unrest.
The Union Ministry of External Affairs is also coordinating to ensure the safety of J&K residents, including students, in Iran.
Jammu and Kashmir Chief Minister Omar Abdullah on Sunday appealed for calm amid widespread protests following the killing of Iran's Supreme Leader Ayatollah Ali Khamenei.
According to officials, protests erupted in several parts of Kashmir after reports that Khamenei was killed in a US-Israel strike. Hundreds of demonstrators gathered in areas with sizeable Shia populations, taking to the streets to voice their anger.
Abdullah said his government is in close coordination with the Union Ministry of External Affairs to ensure the safety and well-being of Jammu and Kashmir residents, including students, currently in Iran.
"Chief Minister has expressed deep concern over the unfolding developments in Iran, including reports of the killing of Iran's Supreme Leader, Ayatollah Ali Khamenei. He has appealed to all communities to remain calm, uphold peace, and avoid any actions that could lead to tension or unrest," the Office of the Chief Minister said in a post on X.
Iranian state media confirmed early Sunday that Khamenei was killed in an attack carried out by Israel and the United States.
The Jammu and Kashmir Pradesh Congress Committee (PCC) postponed all political programmes scheduled for Sunday to honour Khamenei, who was killed in what it described as a joint air strike by the US and Israel.
A PCC spokesperson strongly condemned the air strikes, calling them an inhuman, barbaric, and cowardly act by the US and Israel. PCC president Tariq Hameed Karra led party members in expressing "profound grief and sorrow over this great loss".