JuD leader Abdul Aziz Alvi, who was briefly detained by Pakistani authorities in the aftermath of the 2008 Mumbai attacks, told the protestors: "We will never accept this decision".
The rally was held in the main square of PoK capital Muzaffarabad.
Today's rally comes a day after similar protest was organised in Lahore yesterday.
At the rally in PoK, the protestors, mostly members of the LeT, JeM, JuD and Jamaat-e-Islami, shouted slogans against the Pakistan government and India.
They were joined by supporters of the main opposition PML-N party.
The protesters later blocked the main road in the centre of Muzaffarabad by burning tyres.
Pakistan's cabinet last month said it had approved a proposal to normalise trade ties with India.
Officials have said the process will eventually lead to the granting of Most Favoured Nation-status to India.
The JuD, declared a front for the LeT by the UN Security Council, has been spearheading protests against the move to give India MFN-status.
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