He was born in Marefield, Leicestershire. After Hooker's conversion, his keenly reasoned reflections upon the meanings of Biblical passages and upon the life of a Christian helped his rise into the leadership of the Puritan movement in England. But this status as a leader in the Puritan movement would cause him to emigrate first to Holland and then to New England in 1633, on the ship Griffin, to escape the persecution of Archbishop William Laud for non-conformity. He was appointed the first pastor of the church at Newetowne, Massachusetts (now Cambridge). He is attributed as being the first minister of the First Parish in Cambridge, a church that still exists in the present day. His home was on a plot of land which today is part of the yard at Harvard College. His departure from the Colony of the Massachussettes Bay (the nucleus of the present-day Commonwealth of Massachusetts) was one of the key events leading to the creation of the Colony of Connecticut (the nucleus of the present-day State of the same name).
In 1635, he was appointed by the General Court of Massachusetts to try to persuade his friend Roger Williams to give up his controversial views. Williams took part in a public debate, but Williams refused to change his opinions.
In 1636, Thomas Hooker led 100 of his congregation west to found the new English settlement at Hartford, Connecticut. One of the reasons he left Massachusetts was his failure to agree with John Winthrop about who should take part in civil government. Winthrop held that only admitted members of the Church should vote and hold office; Hooker maintained that any adult male who owned a property should be able to vote and participate in civil government, regardless of church membership.
He and his party, which included Thomas Welles, traveled on the Native American trail that was soon known as the Old Connecticut Path. After settling in Hartford, Hooker continued to be in contact with John Winthrop and Roger Williams. Hooker often traveled to Boston along the Old Connecticut Path, to help settle intercolonial disputes. He is also remembered for his role in creating the "Fundamental Orders of Connecticut". This document is one of the modern world's first written constitutions and a primary influence upon the current American Constitution, written nearly a century and a half later.
His granddaughter Mary Hooker married the Rev. James Pierpont. Their daughter Sarah Pierpont married the Rev. Jonathan Edwards. Some other direct descendants of his included Henry Hooker, William Howard Taft, William Gillette, Edward H. Gillette, George Catlin, Emma Willard, J.P. Morgan, Rev. Joshua Leavitt, Thom Miller, and Adonijah Rockwell.