Johnston founded a grammar school in Durham in 1825,[2] which later merged with other local schools, such as Brandon and Bowburn, to form a single comprehensive school for the area, named Durham Johnston Comprehensive School, preserving James Finlay Weir Johnston's name.[1]
He was appointed reader in Chemistry and Mineralogy at Durham University on its foundation in 1833, but continued to reside in Edinburgh out of term.[2] From 1847, his assistant was Augustus Voelcker who also lectured in agricultural chemistry at Durham University.[5]
In 1849 the Assembly of New Brunswick contracted Johnston to survey and report on potential development.[6] In his Notes on North America, Johnston reported that the Provincial soils were more productive than those of New York or Ohio.
Johnston died in Durham on 18 September 1855.[1] He is buried in the churchyard at St. Bartholomew's church in Sunderland Bridge near Croxdale. Choosing to be buried in a country churchyard rather than in Durham City to avoid polluting drinking water drawn from local springs in the city as his body decayed.[7]