Former Fianna Fáil Minister Barry Andrews has stepped down the as CEO of Goal.
The resignation comes as the charity faces a US inquiry into its operations in Syria. It has been accused of bribery on the Turkey-Syria border.
In August, the Department of Foreign Affairs withheld around €3m in funding from the Irish NGO on foot of a US government investigation into its Syrian aid programme.
The US Agency for International Development (USAID) Office of Inspector General (OIG) is conducting the probe into cross-border aid programs.
"These programs are run from both Turkey and Jordan by multiple nongovernmental organizations (NGOs) with funds from USAID and other international donors", the OIG said in May.
Mr Andrews says he told the Goal board last August of his intention to resign. A replacement CEO is set to be announced in the next few days, starting next month.
Mr Andrews, a barrister, also served as a minister of state for children and youth affairs in government from 2008 to 2011.
In a statement, Mr Andrews said: "The circumstances of the OIG investigation over the last seven months has been extremely uncomfortable for Goal and we are working hard on correcting the weaknesses identified and providing all necessary assurances to our donors.
"I do not for one moment resent the robust oversight of our donor partners and if we are serious about retaining public trust and managing large sums of taxpayers' money, then this type of oversight is not only to be expected, but to be welcomed.
"Goal applies exacting standards to the management of its programmes and in my leadership role over the last few years I have endeavoured to apply those standards.
"However, it has become clear to me that Goal requires a fresh start in terms of leadership. To that end, I informed Goal's board of directors last August of my intention to step down as CEO as soon as a suitable replacement could be identified."
Mr Andrews says he has agreed to continue as interim CEO, while a new appointment will be announced "in the next few days".
Goal chairperson Anne O'Leary, thanked Mr Andrews for his work, adding: "Not only was he largely responsible for helping stabilise the organisation in the months following his appointment; he also led Goal during a period of strong growth.
"The number of people that GOAL has been able to reach has increased during his tenure from approximately four million people across 13 countries at the end of 2012, to 12 million people across 19 countries by the end of 2015."
