In 1949, their first child, David William Thomas was born. John Thomas completed entered high school in St. Catharines, completed his grade 13 curriculum and then enrolled at McMaster University in Hamilton, Ontario, Canada in a Bachelor of Arts program. The Thomas family moved to Toronto in 1950 where John Thomas took the pastorship of Ebenezer Baptist Church on Burnhamthorpe Road, in Etobicoke, Ontario.
Their second child Ian Campbell Thomas was born in 1950. Thomas was the pastor at Ebenezer while he completed his Bachelor of Arts and Bachelor of Divinity degrees at McMaster University.
In 1954, the Thomas family migrated to the United States, where John Thomas won a scholarship at Duke University in Durham, North Carolina in the masters program in philosophy. John Thomas completed the masters and doctorate programs (PhD) at Duke University in 1960. In 1960, the Thomas family returned to Hamilton, Ontario where John Thomas accepted an assistant professorship at the Department of Philosophy at McMaster University. Thomas lectured at McMaster until his retirement in 1993.