Financial consultant Rohaimi Abd Rahim, 37, and car salesman Muhamad Fauzi Misrak, 34, were accused of funding the IS through their blog Revolusi Islam.
They were alleged to have committed the offence in Kampung Baru between March 29 and October 13, The Star reported.
No plea was recorded, though the men nodded to show they understood the charges.
The offence is punishable by up to 30 years in prison and a fine. No bail was granted to them.
Malaysian Muslim woman, Ummi Khalsom Bahok, an assistant credit controller, was charged by a court on October 31 for giving support to the Islamic State (IS) militant group.
She was accused of having committed the offence at an immigration counter at the departure hall of the Kuala Lumpur International Airport on October 5.