Activists of All Parties Hurriyat Conference, Hizbul Mujahideen, United Jihad Council (UJC) and other such group protested to denounce Singh's trip to attend the South Asian Association for Regional Cooperation (SAARC) ministerial conference being hosted by Pakistan.
Syed Salahuddin, the leader of militant outfit Hizbul Mujahidden, who is also chief of UJC, and local leaders of other groups were seen during the protest.
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Another protest was organised by Mishal Malik, wife of Kashmiri leader Yasin Malik, in front of National Press Club here.
On Tuesday, a JuD caravan led by Talha Saeed, the son of Mumbai attack mastermind Hafiz Saeed, had staged a sit-in at the Line of Control near Chakothi in Pakistan occupied Kashmir (PoK), where they were stopped by Pakistani security forces.
The protesters on Wednesday continued their sit-in, demanding that India receives relief materials brought by them for Kashmiris.
A JuD statement said that it has no plans to leave the place unless India receives relief goods, dry food and medicines for the Kashmiris.
Hafiz Abdur Rauf, chief of Falayh-i-Insaniat Foundation, a sister organisation of JuD, said many doctors and paramedical staff were also present in the sit-in.
"These doctors and para-medical staff want to go Sri Nagar to treat our injured Kashmiri brethren," he said.
Various religious and jihadi outfits in Pakistan are opposed to Singh's visit as they held him responsible for the unrest in Indian Kashmir.
Forty-nine people have been killed in Kashmir in clashes since Indian security forces killed Hizbul commander Burhan Wani on July 8.
Earlier, Hafiz Saeed has warned the government that Singh's presence in Islamabad may create "unrest" among Kashmiris as well as Pakistanis in the face of scores of killings in Kashmir.