His son Timothy confirmed the 84-year-old passed away shortly before midnight, Kansas First News reports.
The Westboro Baptist Church gained a repulsive notoriety for picketing the funerals of US servicemen killed in Iraq and Afghanistan.
It claimed the deaths are God's punishment for American immorality and tolerance of homosexuality and abortion.
Phelps's son Nathan who left the group in 1980, revealed his father was dying via Facebook on Sunday.
He also claimed his father had been excommunicated from the church in August 2013.