Boat of Garten was built as a station on the Highland Railway mainline to Inverness via Forres. Its importance was increased on the 1st August 1866, when the Strathspey Railway line from Craigellachie was extended across the river Spey, meeting the Highland Railway halfway between Boat of Garten and Broomhill. Disputes between the two companies resulted in a second parallel track being laid for the Great North of Scotland Railway (operators of the Strathspey Railway) and frequently trains from the two companies would race north from Boat of Garten.

The Highland Railway's mainline from Aviemore to Forres via Boat of Garten and the steep Dava Summit was replaced in 1898 by a direct route between Aviemore and Inverness. In 1965 passenger services on both the Highland Railway line and the GNSR's Strathspey Railway were removed, goods services keeping the Speyside line open until 1968.

In 1972 the Strathspey Railway Company successfully purchased the Aviemore - Boat of Garten section (which was still intact) and reopened the former Highland Railway mainline in 1978. In 2002 the line was extended to Broomhill and in the near future the line should be extended to Grantown on Spey. From trains the divergance of the former Strathspey Railway line to Nethy Bridge and Craigellachie north of Boat of Garten can still be easily seen.

Boat of Garten Station survives as the mid-station on the preserved railway. The former Great North of Scotland Railway engine shed to the north of the station, and the carriage sheds at the end of the platform, have both been demolished.