Jane Ryder, chief executive of the Office of the Scottish Charity Regulator since it was set up in 2003, will step down in September at the end of her contract.
The OSCR published a statement in September 2010 that Ryder would retire in 2011. An OSCR spokesman said this week she would in fact be looking for a new job.
In a statement, Ryder said: "It has always been my plan to leave at this point, with the OSCR firmly established and operational as an effective regulator, and I am ready for new challenges."
The OSCR has appointed a new chair, the Very Rev Dr Graham Forbes, to replace John Naylor, who retired in February.