After deliberating for less than two hours, the jury at Snaresbrook Crown Court unanimously found Dr Patrick Sookhdeo not guilty on Tuesday.
Dr Sookhdeo was arrested in November 2015 on suspicion of an assault on a woman in East London more than 40 years ago.
The charity said in a statement to Premier: "We are thankful for the zeal, vision and integrity with which he has served the persecuted Church for quarter of a century and more."
Dr Sookhdeo stepped down from all roles within the organisation soon after his arrest.
He has previously been found guilty of sexual assault and intimidating witnesses following an incident with a colleague.
Speaking about his departure from the organisation in 2015, Dr Sookhdeo said: "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."
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