The club entered the North Caledonian Football League in the 2006–07 season and originally played their games at Ferry Brae Park in North Kessock and won their first trophy when they beat Golspie Sutherland in the Jock Mackay Memorial Cup.

In Season 2007–08 they again reached the Jock Mackay Memorial Cup Final but were beaten this time on penalties by Golspie Sutherland.

They finally moved into Inverness where their home games were played at the Northern Meeting Park.

In their inaugural season, Inverness City won the Scotscoup Division 2 Junior League and the Elginshire Cup where they defeated Bishopmill United 3–0 in the final to complete an historic double.

[3] After being relegated from the Superleague at the end of the 2017–18 season, Inverness City announced they were taking a year out of Junior football.