Officials from Khan's Pakistan Tehreek-e-Insaf (PTI) party urged supporters to take to the streets after his arrest but police warned that an order prohibiting gatherings of more than four people would be strictly enforced.
It was not immediately clear if Khan was being held at the Islamabad High Court, or had been moved elsewhere.
"Imran Khan has been arrested in the Qadir Trust case," the official Islamabad police Twitter account said, referring to a graft case.
Local TV stations showed chaotic scenes outside the court as hundreds of PTI supporters clashed with security officers.
Khan's arrest comes a day after the military warned him against making "baseless allegations" after he again accused a senior officer of plotting to kill him.
The rebuke late Monday underscored how far Khan's relations have deteriorated with the powerful military, which backed his rise to power in 2018 but withdrew its support ahead of a parliamentary vote of no confidence that ousted him last year.
At a weekend rally in Lahore, Khan repeated claims that a senior intelligence officer Major-General Faisal Naseer was involved in an assassination attempt last year during which he was shot in the leg.
Pakistan's government has said the assassination attempt was the work of a lone gunman, who is now in custody and who confessed in a video controversially leaked to media.
Khan rejects those findings and insists authorities have refused to accept his attempts to file a so-called first information report (FIR) with police identifying the real culprits.
Khan repeated his allegations in a video statement released ahead of his court appearance Tuesday, saying that "there is no reason for me to fabricate the facts".
ISPR said it reserved the right to "take legal course of action against patently false and malafide statements and propaganda".
Khan faces dozens of charges that were brought against him since he was ousted -- a tactic analysts say successive Pakistan governments have used to silence their opponents.
Pakistan's military, the world's sixth largest, holds undue influence over the nation.
It staged at least three coups since the country gained independence in 1947 and ruled for more than three decades.