Kevin Davis will be replaced by Bernard Dan, who led the Chicago Board of Trade for five years until it was taken over by the Chicago Mercantile Exchange last year.
Mr Davis, who led the brokerage for a decade, leaves the company much weakened following its spin-off last year from Man Group, the London-listed hedge-fund manager.
In February, Evan Dooley, a wheat trader at the brokerageâ??s Memphis office, racked up $141m of losses in unauthorised trading, in the largest trading scandal ever to hit agricultural commodity markets.
The incident prompted widespread concern about the companyâ??s risk-management practices. Mr Davis initially blamed the problems on the lifting of control limits on traders, but later evaluation showed that the companyâ??s computer system had not been configured properly.
Investors withdrew an estimated $3.5bn from MF Global in the two months following the incident.
MF Global shares have lost more than 90 per cent of their value during 2008.