He faces three counts of criminal breach of trust and one count of abuse of power. He pleaded not guilty to all counts and has been released on bail.
Mr Najib has long been accused of pocketing $700m (£517m) from the state development fund 1MDB, which he set up.
A new investigation began after his shock election loss in May.
Mr Najib was arrested by anti-corruption authorities on Tuesday and spent the night in detention.
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