In a case that has dragged on for years, Khan's party was accused of receiving funds from abroad, which is illegal in Pakistan, Reuters reported.
Khan was not immediately available for comment but a spokesman for his Pakistan Tehreek-e-Insaf (PTI) party denied wrongdoing.
"We will challenge this ruling," the spokesman, Fawad Chaudhry, told reporters outside the office of the Election Commission of Pakistan in the capital, Islamabad.
Chaudhry said the funds in question were received from overseas Pakistanis, which is not illegal.
Khan was prime minister from 2018 until April of this year when he was forced to step down after losing a confidence vote that he said was the result of a US conspiracy. The United States denied that.
Since then, Khan has been rallying his supporters to press his demand for a new election. The new Prime Minister, Shehbaz Sharif, has rejected that demand.
A spokesman for the Election Commission was not immediately available for comment but media reported that a three-member commission tribunal found that the party got funding from 34 foreigners or foreign companies.
The tribunal said the party had submitted a fake affidavit about its bank accounts, and it had determined that the party hid 13 bank accounts that it should have declared.
The commission asked the party to submit an explanation as to why its funds should not be seized, media reported.
The person who filed the complaint against the party, Khan party founder and former close associate Akbar S. Babar, hailed the ruling.
"All the accusations against Imran Khan have been proven," Babar, who fell out with Khan, told reporters, adding that Khan should step down from the party.