He pleaded not guilty to three counts of criminal breach of trust and one of abuse of power, and was freed on bail.
Mr Najib is accused of taking $700m (£517m) from a state fund he set up.
Police have recovered $273m in luxury goods and cash from raids on properties linked to Mr Najib. He and his wife say the items were legally acquired.
A new investigation into the state development fund 1MDB began after his shock election loss in May.
Mr Najib was arrested by anti-corruption authorities on Tuesday and spent the night in detention.