Self-employed Chong Tat Siong, 23, handphone seller Foong khar Fai, 19, and unemployed Lee phak seng 23, were accused of kidnapping Nayati Shamelin Moodliar, 12, with the intent to get a Malaysian Ringget 300,000 (USD 98000) ransom.
The charge comes under the Kidnapping Act 1961 for abduction, wrongful restraint or wrongful confinement for ransom which carries the death or life imprisonment upon conviction.
No plea was recorded.
Nayati's father Sham Moodliar is ethnic Indian from South Africa while his mother is Dutch. The child holds dual citizenship.
Nayati was bundled into a car by two men while walking to the Mont' Kiara International School on April 28.
He was released six days later at a rest area after the family paid the ransom. The mastermind, still at large, is believed to be in Europe and Interpol is assisting the Malaysian police to track him down.
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Police has managed to recover part of the ransom after nabbing the three men.
Nayati's kidnapping had even prompted premier Najib Razak to express concern via Twitter.
In a show of support, people from around the world had flocked to a Facebook page set up to collect information on his whereabouts.