A statement posted on the organisation's website on Monday read: "It is with great sorrow that the board of trustees of Barnabas Aid International announce the resignation of Dr Patrick Sookhdeo as a trustee of Barnabas Aid International and from his positions as International Director and CEO of Barnabas Fund as of 22nd November 2015.
"Dr Sookhdeo founded Barnabas Fund and has led it with zeal, vision and integrity for 22 years. We are immensely grieved that current circumstances oblige him to step down."
The announcement comes just months after he was found guilty of sexual assault and intimidating witnesses following an incident with a colleague. Just weeks ago a number of critical articles appeared on the website Christian Today.
Revd Paul Mursalin has been appointed Acting International Director and Hendrick Storm will take over as CEO.
Speaking about his departure, Patrick Sookhdeo said: "It has been a privilege to serve the persecuted Church for many years. I have always been motivated by the needs of Christians facing suffering.
"I hope for many years to come I can continue serving those whom the world often doesn't notice. My inspiration has always been Barnabas, the encourager, who stood up for the suffering saints of the early Church. Please pray for me, as I pray for others."
Barnabas Fund works with persecuted Christians across the world. It is currently supporting thousands of believers fleeing Iraq and Syria.