In the following year he entered into a partnership with Samuel Woodgate Durrant, which lasted till 1828, when he removed to 25 Tokenhouse Yard.
The Report presented by the Commissioners in 1838 states, "Our first step in the execution of the duty thus confided to us was to choose Mr. John Southerden Burn for our secretary".
[2] In 1857, Burn was himself appointed a member of the Commission which he had previously served as secretary, at the same time as George Graham, Registrar General from 1842 to 1880, and the barrister Horace Mann, who had compiled the Report on the Religious Census of 1851.
In 1831 he published, with biographical notes, the Livre des Anglois à Genève, the register of the English church in Geneva from 1554 to 1558, which had been communicated to him by Samuel Egerton Brydges.
In 1846 he issued his major work, The History of the French, Walloon, Dutch, and other Foreign Protestant Refugees settled in England, which he compiled mainly from registers of places of worship.
In 1865 he produced The High Commission, dedicated to Charles George Young, which consisted of a collection of notices of the court and its procedure drawn from various sources.
Early in 1870, he issued a similar but more elaborate work on The Star Chamber, which also contained some additional notes on the court of high commission.