The accused trio of architect Mohd Syafrein Rasid (26), trader Mohd Rosmadi Che Daud (42) and technician Mohamad Yusoffe Ishak (26) were charged with allegedly taking a Qatar Airways flight from Kuala Lumpur International Airport to Istanbul with intentions of giving support to the IS and becoming its members.
The three men allegedly committed the offence on September 25 this year.
They were also charged with an alternative count of trying to benefit IS by taking the same flight, New Straits Times reported.
Malaysian authorities arrested 14 people earlier this month for suspected terror links.
At least 40 Malaysians are believed to have left for Syria to join IS militants.