The Ffarquhar Branch Line, also known as Thomas' Branch Line, runs between Knapford and Ffarquhar, which he was awarded after recovering James from an accident. He loves it dearly and considers it the pride of the railway. The section between Knapford and Elsbridge was the original route 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, horses were replaced by steam engines. In 1915, a bay platform was opened at Knapford and was connected via a branch. After 1923, Thomas was sent to run the line. The run down of the lead mines at Toryreck began in 1925, but opportunities of stone traffic from Ffarquhar opened and the line to Elsbridge was extended. The lead mines at Toryreck closed in 1930. 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' branch line starts from Knapford Junction where it connects with the Main Line. It then calls at Dryaw, Toryreck, Elsbridge and Hackenbeck before terminating at Ffarquhar. In the television series, Maithwaite is located between Elsbridge and Hackenbeck.
The branch carries passengers, quarry stone, farm produce, dairy products from St. Pedroc's Dairy in Elsbridge, general goods and uranium from the mines. Some passenger trains work into Tidmouth to pick up a through coach from the Wild Nor' Wester. Thomas and formerly Daisy run passenger duties with Annie and Clarabel. Toby, with Henrietta, Victoria and Elsie, run trains to Anopha Quarry.
The branch also has a goods-line from Toryreck to Knapford Harbour, worked by Percy, who 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".
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.