Tokyo Stock Exchange president Takuo Tsurushima has resigned following a 40bn yen ($333m; £190m) trading error.
Mr Tsurushima has accepted responsibility for the trading error
This month the exchange's computer systems failed to cancel a mistaken order to sell 610,000 shares for 1 yen, instead of one share for 610,000 yen.
The trade in shares of recruitment firm J-Com was done by Mizuho Securities and dented the reputation of the exchange.
It came only weeks after a computer glitch caused the world's second largest market to close for four hours.
The stock exchange's problems come at a time when it is considering plans to float its own shares next year.
'Trust of the market'
When the trader realised he had made an error in the J-Com order, which happened on 8 December, Mizuho tried repeatedly to cancel the transaction, but a fault in the exchange system prevented them from doing so.
Mr Tsurushima, 67, said he was accepting responsibility and stepping down.
"I apologize to investors and officials concerned for the confusion in the markets," Mr Tsurushima said.
"We have made this decision in order to clarify the management's responsibility."
He added: "The Tokyo Stock Exchange will try to do its best to gain the trust of the market."
Also stepping down are Sadao Yoshino, who is in charge of the stock exchange's computer system, and its managing director and executive officer Tomio Amano.
The stock exchange's chairman Taizo Nishimuro will take over as chief executive.
Pressure to step down had increased on Mr Tsurushima after shares in J-Com tumbled because of the trading error.
Prime Minister Junichiro Koizumi called for new safety measures and the market's watchdog launched an investigation into what went wrong.
The brokerage managed to repurchase the majority of the phantom shares it sold, but the error has cost it billions of yen in losses.