Loch Ness were formed in 1999 by current manager Shane Carling, and for 20 years played as members of the welfare/amateur recreational leagues of Inverness & District.

During the summer of 2020, the club received widespread acknowledgement via social media after releasing prototypes for their new kits, which featured the Loch Ness Monster in the pattern.

[3][4] The designs were subsequently used and made by Lancashire company Zero Negativity Clothing, receiving orders worldwide upon release.

As part of a sponsorship deal with WooHa Brewing Company, the sponsor created a limited edition lager named for the club.

In the 2022–23 season, Loch Ness won the North Caledonian League title for the first time in their history with a 5–0 win over Fort William, the title also meant they qualified for the Scottish Cup for the first time, where they drew, and lost 3–1 to, Luncarty of the East of Scotland Premier Division.