The body of Gowhar Ahmad Bhat, district president of the BJP's youth wing, the Bhartiya Janata Yuva Morcha, was found with the throat slit at Killora village in the district after he was abducted by unidentified terrorists from a government hospital. Officials say he was a health department employee.
Police say they are investigating which terror group is behind the killing.
This is the second such brutal execution by terrorists in Shopian in last three weeks. Earlier, school teacher Aijaz Ahmad Lone's throat was slit by terrorists who accused him of being an informer for security forces.
The BJP and other political parties have strongly reacted to the gruesome murder.
In a series of tweets last night, BJP President Amit Shah condoled Mr Bhat's death by saying that terrorists could not stop the youth from choosing a better future.
"Pained to learn about the brutal murder of our @BJYM District President Gowhar Ahmed in Shopian, J&K. My deepest condolences to his family. Terrorists must realise that they cannot stop the youth of the valley from choosing a better future for themselves," Mr Shah tweeted.
National Conference leader and former Jammu and Kashmir Chief Minister Omar Abdullah tweeted, "How tragic. A young life snuffed out in such a heartless way just adds to the sense of shock. Allah jannat naseeb karey."
Mr Bhat is the second political activist killed by terrorists in the same area. Last month, a PDP worker and a former sarpanch was shot dead by terrorists.
More than 5,000 political workers, mainly from National Conference, have been killed in Kashmir in the last near three decades of violence.