Thomas was educated at Gonville Hall, Cambridge (later becoming Gonville and Caias College) graduating with a B.A. 1517-8, an M.A. in 1521 and a D.D in 1556-7. He was a scholar from Michaelmas 1517 to 1519 and a fellow from 1519 to 1527. He was principal of Physwick Hostel, part of Cambridge University, in 1521. In 1546 Physwick and St Margaret's were merged into the new Trinity College by Henry VIII along with Michaelhouse College, King’s Hall and five other hostels: Gregory’s, Ovyng’s, Catherine’s, Garratt, and Tyler’s.
Thomas became the fifteenth master of Gonville Hall in 1552. When in 1557 John Caius refounded Gonville Hall as Gonville and Caius College, Caius' statutes appointed Bacon Master of the new foundation on the 4th September 1557. Caius' character assessment of Bacon was not positive: homo certe gravis, mitis, et amabilis, sed custos inutilis et negligens (certainly a serious, gentle, and amicable man, but a useless and negligent custodian). When Thomas died he was succeeded as Master by John Caias.
He was the Rector of Hockwold from 1529 to 1539 and Chaplain to Henry VIII who presented him to the Rectory of Barrow, Suffolk in 1539.
From 1528 to 1554 he was vicar of Hoxne, becoming Rector of Brandon in 1554.
He was also Canon of Stoke by Clare and Cannon of Ely in 1544 and Rector of Chelsfield, Kent from 1532 until his death. He died at Chelsfield on 1st January 1558/9 and is buried there. The entry in the parish register being simply 'Thomas Bacon, parson, there buried, Jan. 3, 1558'
He died intestate and an inventory of his goods was taken, presumably at his Lodge in Cambridge, with total value of £12. 0. 7.
He died deeply in debt and had fraudulently disposed of his property by deedto his brother Nicholas, a merchant in London, shortly before his death.