Gilbert Deya, a former stonemason who moved to London from Kenya in the mid-90s, was accused of stealing five children between 1999 and 2004 to buttress his claims.
Senior Principal Magistrate Robison Ondieki found the 86-year-old not guilty, ruling that the prosecution had not produced enough evidence to link Deya to the charges.
The preacher, whose Gilbert Deya Ministries had churches in London, Birmingham, Nottingham, Liverpool and Manchester, was extradited from Britain to Kenya in 2017 following a decade-long legal battle to remain in the UK.
Deya and his wife Mary claimed their prayers could see infertile and post-menopausal women become pregnant in four months, and without intercourse.
However prosecutors said the "miracle babies" were stolen, mainly from Nairobi's poor neighborhoods.
"I have been acquitted of this burden, a yoke on my shoulder," Deya told reporters outside the court, adding that it was "sad that I have been labelled as a child stealer."
"It damaged my reputation."
Deya's lawyer, John Swaka, told AFP, "the charges were trumped up and could not stand in a court of law."
"He is delighted and very happy. He has no squabbles with anyone and will go back to serving the Lord."
A predominantly Christian country, Kenya is home to around 4,000 churches, including some run by self-styled pastors with no theological education.
The discovery in April of bodies linked to a Kenyan cult that practiced starvation to "meet Jesus Christ" has prompted questions about the need for more regulation of religious outfits in the East African nation.
Nearly 400 bodies have been found so far in the Shakahola forest in coastal Kenya, with cult leader and self-proclaimed pastor Paul Nthenge Mackenzie in police custody since mid-April.