Hutchinson was born in Carsington, Derbyshire, the second son of Mary and Edward Hutchinson or Hitchinson (a family of the lesser landed gentry). He was taught history by his uncle, Francis Tallents, a Puritan clergyman, before beginning his studies at Katharine Hall, Cambridge at the age of 18. He graduated B.A. in 1681 and M.A. in 1684, a year after he was ordained by the bishop of London and was appointed Lecturer at the rectory of Widdington, Essex. This living represented the lowest rung of the career ladder of the Church of England and Hutchinson remained there until appointed vicar of Hoxne, Suffolk in early 1690 by local Whig magnate, William Maynard.
He studied several cases of witchcraft and witch trials, criticising some procedures. For example, he opposed the idea that children and young teenagers acted as accusers in cases of bewitching after having reached the conclusion that they feigned demon possession and several innocents had died for that reason, and wrote a book that ended the persecution of witches in England.
Hutchinson was later named bishop in Scotland and continued writing on the subject, and criticised severely the works of Jean Bodin, whom he considered a very foolish man. Hutchinson is referred to as "Europe first classical liberal." He advocated reason rather than divine revelation be used in worship of Deity. Hutchinson provide an opposition to the fundamentalist Scottish Kirk.