The women, Doan Thi Huong from Vietnam and Siti Aisyah from Indonesia, allegedly smeared deadly VX nerve agent on Mr Kim's face in Kuala Lumpur airport on 13 February.
They appeared in court near Malaysia's capital, protected by special forces.
They could face the death penalty if convicted of murder.
No plea was recorded in the magistrates' court as only higher courts have jurisdiction over murder cases. But after the charge was read out, Doan Thi Huong said "I understand but I am not guilty," in English.
It is widely believed that North Korea was responsible for the attack, which it fiercely denies. Kim Jong-nam, was openly critical of the North Korean regime.