At the start of season 2003-2004 the league was due to consist of 11 clubs when Inverness City were elected to replace Alness United who had applied to join the Scottish Junior Football Association's Northern Region. However Alness' application was unsuccessful and they returned to the NCFL. The league returned to the rounder number of 10 clubs when Inverness City withdrew at the last minute owing to their failure to secure a viable ground to play their home fixtures at.
The start of the 2005-2006 season saw the withdrawal from the league of Tain St. Duthus due to financial problems, reducing the league to only 9 teams. It was hoped that this would be a mere season's abeyance, but they did not re-enter the following season, and have now gone out of existence entirely. They are succeeded by Tain Thistle.
Inverness City finally joined in 2006-2007 season having found a home ground at North Kessock. However, the league was left with the uneven number of 9 clubs as Bonar Bridge withdrew from the competition. The league title was won by Golspie Sutherland.
The 2008-2009 season will start with ten teams. This is due to the withdrawal of Dornoch FC and Inverness City joining the Junior leagues. The league is also joined by newcomers, Tain Thistle.
The NCFL is characterized by the number of clubs who use it as a 'stepping-stone' to try and either join the Highland League or join the 'junior' grade of football.
