Judge Syed Kausar Abbas Zaidi issued the orders for Khan, Qadri and 26 other people at Islamabad's Special Anti-Terrorism Court on Wednesday, a court official told AFP.
Weeks of protests led by Khan and Qadri seeking the resignation of Prime Minister Nawaz Sharif descended into several days of violence at the end of August.
Demonstrators clashed with police, attempted to storm parliament and briefly took over state broadcaster Pakistan Television (PTV), taking its news channel off-air for a while.
A police spokesman told AFP no arrests had been made so far, but cases had been registered under anti-terrorism laws for attacking PTV, parliament and other official buildings, and clashing with police.
Qadri called off his protest last month and has left for Canada, where he is normally based, but Khan continues to address supporters from the top of a shipping container outside parliament most evenings.
The protests destabilised Sharif's government for a while but have so far failed in their stated aim of bringing down his administration.
Khan has announced a fresh protest rally in Islamabad on November 30.
Shireen Mazari, spokeswoman for Khan's Pakistan Tehreek-e-Insaaf (PTI) party, dismissed the warrants as an act of desperation by the government.
On the day PTV was stormed, September 1, an AFP reporter saw more than 300 protesters, many armed with wooden clubs, enter the building shouting anti-government slogans.
Television footage showed some of them beating a photo of Sharif with sticks and spitting on it.
Several people at the scene were wearing PTI scarves and t-shirts, and Khan apologised, saying his party workers had "become emotional".
Rasul Baksh Rais, a political analyst, said the judge was probably not influenced by the government in his decision to issue the arrest warrants, since apprehending Khan and Qadri would reinvigorate their followers.
"The Pakistani system is very complex. The accused can go to a higher court to seek bail before the arrest takes place," he said.
"I do think the government will wait to act to implement the order to give (Khan and Qadri) time to seek bail."
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