Deacon Thomas Burnham, Jr. was the second son and middle child of Thomas Burnham, Sr. (1686-1742) and his wife Hannah (Cogswell) Burnham Choate (1693-1782). After being widowed, his mother remarried to Captain Thomas Choate, a widower. There were no children from that union.

Thomas first married Lucy Cogswell, daughter of William Cogswell (1694-1762) and his wife Mary (Cogswell) Cogswell (1699-1734). Thomas and Lucy married in Ipswich, Massachusetts on January 17, 1750. This marriage produced 7 children. These children included the following:

-William Burnham (b.1751) m. Rachel Andrews (b. 1759), dau. of Joseph Andrews (1729-1806) and his wife Rachel (Burnahm) Andrews who was William's paternal aunt making wife Rachel his first cousin.
-Thomas Burnham III (1755-1804) m. (1st) Hepsibah Pearson (1757-bef. 1793) - 5 children. (2nd) Ruth Cavis (b. 1757) - 4 children.
-Lucy (Burnham) Burnham (1757-1844) m. Captain Nathaniel Burnham (1755-1842) - 9 children to reach adulthood.
-Esther (Burnham) Butler (b. 1763) m. Ralph Butler (b. 1760) - 8 children.
-Abraham Burnham (1763-1810) m. Hannah Pulsifer (1777-1852) - 2 sons.
-Hannah (Burnham) Cogswell (1767-1847) - 2 daughters.
-Luther Burnham (1772-1774).

After Thomas was widowed, in 1775, he remarried three years later to second wife Elizabeth Burnham whom he married on June 11, 1778 in Ipswich. Elizabeth Burnham was 30 years younger than he. Elizabeth was the daughter and one of the youngest children of Samuel Burnham (1721-1772) and his wife Martha (Story) Burnham (1721-1761). Thomas's second marriage with Elizabeth produced five more children. However, none of these children survived to adulthood but one youngest child Stephen Burnham (1786-1838). Stephen married Lois Story (1788-1861) with whom he had 7 children.