A presidential decree said on Saturday, Cetinkaya, who was appointed in April 2016, has been replaced by Murat Uysal.
The move came after months of tension with the government over high interest rates. However, the official decree gave no official reason for the change.
President Erdogan has repeatedly railed against high interest rates and called for them to be lowered in a bid to stimulate growth.
Turkey’s main interest rate is 24 per cent after the bank under Cetinkaya made an aggressive rate hike of 625 basis points last September following a currency crisis in August.
Last month, President Erdogan said high interest rates harmed Turkey.