He was promoted in 1855 to become the district engineer for the GNR's loop line and then again in 1859 to take responsibility for the Peterborough to Doncaster route.

In 1861 he became chief engineer to the GNR upon the retirement of his predecessor Walter Marr Brydone.

He went on to oversee the construction of the GNR Derbyshire and Staffordshire Extension, which involved several significant bridges, including Giltbrook Viaduct in Nottinghamshire, Bennerley Viaduct near Ilkeston on the Nottinghamshire–Derbyshire border, and two in Derby: the Handyside Bridge over the River Derwent and the Friargate Bridge carrying the approach tracks to Derby Friargate railway station, as well as the Kimberley Cutting.

[2] In his personal life, Johnson was teetotal, avoiding all forms of alcohol, and a Christian missionary.

[1] His son, T R Johnson, was GNR Assistant Engineer and, from 1907 to 1914, New South Wales Chief Railway Commissioner.