The Morayshire Railway was first suggested in the 1840s as a railway connecting the city of Elgin and the port of Lossiemouth. At the time it was also proposed to extend the railway 16 miles south of Elgin to Craigellachie, in Strathspey. Before a bill could be lodged the Great North of Scotland Railway announced its plans for a railway from Aberdeen to Inverness. As the two railways would share a large proportion of the route south of Elgin to Morayshire reached an agreement to use the new GNSR line south of Elgin and bridging off at Orton to serve Craigellachie.

However the financial panic of the 1850s delayed the GNSR scheme, and in 1851 the board of the Morayshire Railway decided to abandon the Craigellachie extention. This led to fierce criticism and almost caused the collapse of the company, however it was eventually able to start construction of the 5 1/2 miles between Elgin & Lossiemouth in 1851. The line opened on 10 August 1852, and was thus the first railway in the future Great North of Scotland Railway district to operate.

The Great North of Scotland Railway powers lapsed in 1854 and the Morayshire began to look towards building the Elgin-Craigellachie section by themselves. However the Inverness & Aberdeen Junction Railway eventually announced that it would construct the remainder of the route to Inverness and thus the earlier plans for a junction at Orton were used. Powers to construct the Orton - Craigellachie section were granted on 18 July 1856 and the section between Orton and Rothes was opened on 23 August 1858. The remainder of the extention opened on 23 December 1858.

Disputes with the Inverness & Aberdeen Junction Railway led to the Morayshire planning a separate route between Elgin and Rothes, and began to negociate with the Great North of Scotland Railway (bitter rivals of the Inverness & Aberdeen Junction) to help construct the new line. To the GNSR the advantage of a separate route to Elgin was obvious and they offered £20,000 towards the cost of the new line. The line opened to goods traffic on 30 December 1861 and to Passenger trains on 1 January 1862. The new line was actually shorter than the route via Orton and the Inverness & Aberdeen Junction Railway (later the Highland Railway).

On 17 May 1861 the Morayshire Railway was authorised to extend from Craigellachie across the river Spey to the Strathspey Railway. Together with the Keith & Dufftown Railway this would allow the GNSR a separate route to Elgin and with the opening of the Strathspey & Morayshire extentions on 1 July 1963 the GNSR took over the working of the entire Morayshire Railway system. On 30 July 1866 an act was passed authorised the amalgamation of the Morayshire Railway into the Great North of Scotland Railway, and on the 31 July services between Orton and Rothes were removed. The junction with the Highland Railway was severed and for some years goods were worked between Rothes and the intermediate siding at Sourden. The line eventually became overgrown and was removed in 1907.
Meanwhile, fusion with the GNSR was delayed until 1 October 1888. Just north of Elgin the Morayshire Railway was eventually joined by the Moray Coast Railway from Portsoy. In 1968 British Railways withdrew passenger services along the Coast Line and the "Glen" line - the former Morayshire/Keith & Dufftown Line via Craigellachie.