Thomas's Branch Line was given to Thomas after saving James in an accident in 1923. It runs from Knapford to Ffarquhar, where it branches off to a quarry, and a possible extension to Ulfstead. The section between Knapford and Elsbridge was originally part of the Tidmouth, Knapford, and Elsbridge Railway.
A harbour line from Elsbridge to Knapford was opened in 1885 and used horse-pulled wagons. Later after (or before) the Tidmouth, Wellsworth and Suddery Railway and the Sodor and Mainland Railway were joined into the North Western Railway the horses were replaced by steam engines. In 1915 a bay platform was opened at Knapford and was connected via a Branch. After 1947, Thomas was sent to run the line.
The lead mines at Toryreck closed in 1930, but opportunities of stone traffic from Ffarquhar opened and the line to Elsbridge was extended. In 1956, the improvement scheme of the harbour at Knapford was started, the branch to the harbour was rebuilt on an easier gradient and the stations were moved north of the river. The harbour line is now used for goods.
Thomas and Daisy run passenger duties with Annie and Clarabel. Toby, with Henrietta, Victoria, and Elsie, run trains to Anopha Quarry. Percy is in charge of goods duties, although when Thomas is absent he takes over passenger duties. He and Toby also appear to share the workload of stone trains to Knapford Harbour. Stepney, Duck, Wilbert, and Emily have also worked on the branch at various points. Edward once made a trip to the quarry before the policeman stopped Thomas for being "unsafe".
The branch also has a goods-line from Toryreck to Knapford Harbour, worked by Percy. This line also has a connection to the Dryaw mines, formerly used for mining lead but now being worked for deposits of uranium.
The quarry tramroad extends five miles from Ffarquhar, through the streets of the village, then into the hills to the private sidings of Anopha Quarry. This tramway is property of the North Western Railway and was formerly worked by Toby, but more recent arrangements have allowed for Mavis to operate trains on it.
In the television series, it continues to the Mountain Village, and Maithwaite.
At Day, it is inhabited by Annie & Clarabel.
At Dusk, it is inhabited by Roley the Coach.
At Night and the Flooded version, it is inhabited by Thomas.