James Deutsch, who has run the organisation for the past five and a half years, is leaving to take up a new job based in New York.
Gail Cookson, who leaves her job as client services director at direct marketing agency WWAV Rapp Collins next month, will take on the role of interim chief executive at Crusaid until a permanent appointment is made.
"Gail is a highly proficient fundraiser and the organisation will benefit tremendously from having her in a more hands-on role for a few months,
said Deutsch. "However, Gail is not applying for the permanent post and we don't have anyone lined up internally.