The indictment was the latest in dozens of cases against the 72-year-old former cricket star turned politician, who has been in jail since late last year.
It came hours after a court issued warrants to arrest Khan's wife.
Khan pleaded not guilty as the judge in an anti-terrorism court in Rawalpindi read out the charges against him and dozens of others including his former ministers, leaders and supporters, local media and his party said.
The party said it would challenge the indictment.
"The indictment came without any proof or evidence. Once we challenge it we are confident it will be thrown out as it is nothing but political victimisation," a spokesman for Khan's Pakistan Tehreek-e-Insaf (PTI) party said.
The spokesman, Zulfikar Bukhari, said it was not clear yet what maximum punishment Khan could face under the terrorism charges.
Khan is currently on trial on corruption charges although all of his sentences have either been suspended or overturned.
Thousands of Khan's supporters attacked and torched several military buildings and offices, including the military headquarters in Rawalpindi, on May 9, 2023 in a protest against Khan's arrest on graft allegations.
At least eight people were killed in the violence.
Khan has previously denied that he directed the attacks.
The attacks were an unprecedented challenge to the military in Pakistan, which has long played an outsized role in the country's politics.
Several of Khan's supporters have already been sentenced in connection with the violence.
A former government minister, Omar Ayub Khan, who is at present the leader of opposition in parliament, was arrested shortly after the indictment outside the jail, the party said.
Khan has been fighting court cases since he was ousted from power in 2022.
He and his party say the cases were made up to keep him out of politics at the behest of the military after he had fallen out with the army's generals.
The army denies the accusation.
His party has organised multiple protests over his imprisonment, demanding his release and the resignation of the government it says was formed through a rigged election earlier this year.
The government denies the rigging accusation.
Khan's wife, Bushra Bibi, led a deadly protest march by thousands of supporters in the capital Islamabad on November 25, escalating a face-off with the government and its military backers.
A court on Thursday issued warrants to arrest her for not appearing in a graft case despite repeated summons.
