Thomas Boston, the younger (1713–1767) was a Scottish minister of the Relief Church.
The youngest son of Thomas Boston (1677–1732), he was born at Ettrick on 3 April 1713, After some home instruction, he went to the grammar school at Hawick, and then to Edinburgh University.
Boston was licensed on 1 August 1732 by the Selkirk presbytery, presented to Ettrick in place of his father in November 1732, and ordained there on 4 April 1733. On 25 October 1748 he was released from the charge, having a call to Oxnam, Roxburghshire; and was admitted there on 10 August 1749.
Popular as the heir to his father's theology of the Marrow Controversy, Boston was the immediate cause of a rift in the parish church of the neighbouring town of Jedburgh. When a vacancy there was filled over the wishes of the congregation, the elders of the church and most of the parishioners, including the town council, withdrew from the church and built a meeting-house for Boston.
John Bonar, who had been appointed to Jedburgh, did not take up the post. Boston tendered his demission to the presbytery on 7 December 1757. On 30 May 1758 the General Assembly of the Church of Scotland accepted his demission, and in doing so declared him henceforth incapable of receiving a presentation; and prohibited all ministers from employing him in any office.
Boston then continued his ministry at Jedburgh as an Independent. In 1761 he and Thomas Gillespie joined in admitting Thomas Colier as minister to a congregation at Colinsburgh. The three constituted themselves into a new body, the "Presbytery of Relief". Boston was its first moderator. In 1765 he went to Glasgow, on trial as a minister to a Relief congregation there, but was not called.