James Alison was born in 1959, the son of Michael Alison and Sylvia Alison (née Haigh). He has a brother and a sister. In Faith Beyond Resentment he describes his family background as "conservative middle-class English evangelical Protestant". His father was the Rt Hon Michael Alison (died 2004), who, after leaving Oxford University, had spent some time studying theology at Ridley Hall and had gone on to become a prominent Conservative Member of Parliament (1964–1997) and Second Church Estates Commissioner (1987-1997). Alison left the Church of England at the age of eighteen, to join the Roman Catholic Church. He studied at Blackfriars College at the University of Oxford, and earned his bachelor's degree and doctorate in theology from the Jesuit Theology Faculty in Belo Horizonte, Brazil.
Alison was a member of the Dominican order – his master's degree is a Dominican lectorate – from 1981 to 1995. He has lived and worked in Mexico, Brazil, Bolivia, Chile and the United States. Currently he works as a travelling preacher, lecturer and retreat giver, based in São Paulo, Brazil.
Alison says that his disagreement with the official Roman Catholic Church teaching on homosexuality is based on official Catholic teaching concerning nature, grace and original sin (see homosexuality and Roman Catholicism).