Nor Shamsiah, who was formerly deputy governor, left Bank Negara after her term ended in November 2016.
She replaces Muhammad Ibrahim, who stepped down on June 6 just two years after he was appointed.
Prime Minister Dr Mahathir Mohamad, who confirmed Muhammad’s resignation, said he had given no concrete reason for stepping down.
Muhammad, a career banker, took over from Zeti Akhtar Aziz in May 2016.
His resignation followed Finance Minister Lim Guan Eng’s revelation last month that funds from a land sale made by the government to the central bank for about RM2 billion had been used to pay for 1MDB’s obligation to Abu Dhabi state fund IPIC.
BNM had said the transaction complied with government requirements and that it had handed details of the deal to the anti-graft agency.