Balmer was born at Ormiston Mains, in the parish of Eckford, Roxburghshire on 22 November 1787.
He entered the University of Edinburgh in 1802, and in 1806 the Theological Hall at Selkirk, under George Lawson of the Secession Church.
In 1812 he received licence as a preacher from the Presbytery of Edinburgh, and in 1814 was ordained minister in Berwick-upon-Tweed, where he remained till his death.
When certain discussions arose among his brethren on some Calvinistic doctrines, he supported the less stringent views.
At a meeting held in Edinburgh in 1843, to commemorate the bicentennial of the Westminster Assembly, he delivered a speech in favour of Christian union, which attracted the attention of Thomas Chalmers and others, and led to important measures being taken by John Henderson of Park for promoting that cause.