Steve Vaughan, the chief executive of Misys' banking systems division, has left the company after just one month in the job.
In a short statement, Misys says Vaughan is to leave the company by mutual agreement with immediate effect.
Misys says it had become clear that there are "material differences" between Vaughan and the company as to the future direction of the banking systems unit. Given this, the Misys Board and Vaughan have agreed that it is appropriate for him to leave the company at this point.
For the time being, Misys group chief executive Kevin Lomax will resume Vaughan's responsibilities until a replacement is found.
Vaughan - who had previously worked at Synstar and EDS - took up the position of CEO of Misys' struggling banking systems unit on 20 March, replacing Ivan Martin who stepped down in December.
He was brought in to oversee a broad restructuring at the division, which reported a shock 25% decline in first half operating profits in January. As part of this, Vaughan was expected to assume responsibility of Misys' new core banking unit, which will be created by the merger of its retail and wholesale banking operations.
Market analysts interpreted the move as an indication that the company may nmot yet be prepared for the kind of radical surgery required to turn the business around. Misys denies that the differences of opinion that sparked Vaughan's departure involved any discussion of a possible sale of the banking systems business.
Misys shares were down 5.75 pence to 211.75 pence in morning trading.