Thomas Danforth was baptized 20 Nov. 1623 at St. Michael's in Framlingham, son of Nicholas Danforth (1589-1638) and Elizabeth Barber (d. 1629). He came with his father and siblings and settled in Cambridge, Mass., in 1635. He married in Cambridge 23 Feb. 1643 Mary Withington (d. 1697), daughter of Henry Withington (1590-1667) and Elizabeth Smith (d. 1660). Thomas and Mary had 12 children, but six of their children died before the age of 3, and Danforth was survived by only three children.

Thomas Danforth was deputy governor of Massachusetts Bay Colony 1679-1686 and 1689-1692; magistrate of the Superior Court of Judicature 1692-1699; president of the district of Maine 1681-1692; Assistant 1659-1678; recorder for Middlesex county court 1648-1686; treasurer of Harvard College 1650-1669; Cambridge selectman 1645-1671 and town clerk 1645-1668.

As deputy governor, Danforth observed the examinations of accused witches Elizabeth Proctor and Sarah Cloyce in Salem in April 1692—which was before the Court of Oyer & Terminer was established for the actual trials. He disapproved of the proceedings, and by October 1692, openly condemned the trials, according to his friend Thomas Brattle. In early December 1692, Danforth was "pressed" into accepting a position as a magistrate of the Superior Court of Judicature, which handled the remaining witch trial cases. Three women were convicted of witchcraft during the January 1693 trials, but were reprieved by Gov. William Phips. He remained on the SCJ until his death in 1699.

Danforth gave 800 acres of his land to families of Salem witch trial victims, in an area known as Salem End in Framingham, Massachusetts.

The Diary of Samuel Sewall (1:504-505) includes mention of Thomas Danforth's illness, death, and burial. "Sixth day, Nov. 10, 1699. Mr. Danforth is entombed about 1/4 of an hour before 4 P. M. Very fair and pleasant day; much company. Bearers: on the right side, Lt-Governor, Mr. Russell, Sewall; left side, Mr. W. Winthrop, Mr. Cook, Col. Phillips. I helped lift the corpse into the tomb, carrying the feet. Had cake and cheese at the house. Col. Hathorn, Mr. Corwin, Bro. Sewall were there from Salem. Councilors had rings, ministers gloves, Mr. Mather and Brattle scarfs and rings: so had the bearers. Cambridge Burying Place is handsomely fenced in with boards, which has not been done above a month or six weeks." While it doesn't explicitly say which tomb Danforth is in, and none are labeled with his name, he's definitely buried here. His wife and possibly other family members may be buried there too.