The club was founded in 1972 by then chairman Colin Neilson and started out playing mainly friendlies and cup competitions, such as the Scottish Qualifying Cup, the North of Scotland Cup and the Inverness Cup. This lasted for 11 years, before they joined the North Caledonian Football League (NCFL) in 1983. They enjoyed a lot of success in their brief two-year spell in the North Caledonian League winning both the Chic Allan Cup and Morris Newton Cup in successive seasons, while also winning the Football Times Cup and finishing as runners-up in the league in the 1983–84 season. However the season after, 1984–85, they would go on to win the division outright making it their only League Championship to date.
Ever since forming in 1972, the club had tirelessly campaigned for entry into the Highland League, but were rejected many times before the club were admitted in the North Caledonian Football League in 1983. However, after accomplishing a lot of success in their two-year spell in the North Caledonian League, the club were finally given entry and would begin life as a Highland League club for the 1985–86 season.
The Fort played their first-ever Highland League match against nearest rivals Clachnacuddin from Inverness in a game in which the Fort won with then young striker Gordon MacIntyre scoring their first-ever Highland League goal in a 1–0 home win. Later on that season in early January 1986, the club recorded its highest-ever attendance of about 1,500 when they entertained Scottish Football League side Stirling Albion F.C. in the Scottish Cup Second Road, holding them to a 0–0 draw, before losing 6–0 in the replay at Annfield a week later.
Prior to the days of the Highland League and even the North Caledonian League, the Fort probably produced their most famous player to date. In the late 1970s, a very young player by the name of John McGinlay made his senior debut for the club at the age of 14 coming on as a substitute in a North of Scotland cup tie with now Scottish Football League side Elgin City, formerly of the Highland League. At the age of 17, he left the Fort to join up with Nairn County and would later go on to play in the Premier League with Bolton Wanderers and even represent Scotland as a full international. He was also childhood friends with another now former professional footballer Duncan Shearer, who also hailed from Fort William, but instead played for the Inverness-based side Clachnacuddin.