[9] However Northern lost the "rough and tumble sort" of replay at Hampden Park by six goals to nil;[10] Queen's went on to win the trophy.

Despite this lack of success, Northern was one of the five clubs which agreed to set up the Scottish Football Alliance in 1891,[14] to provide regular league competition.

After two mediocre seasons, Northern (and a number of other Alliance members) accepted an invitation to form the new Division Two of the Scottish League.

1893–94 proved to be their sole season in the league, with the club finishing ninth out of ten, and failing re-election, losing on a fourth ballot by 1 vote to Airdrieonians.

[15] It returned to the Scottish Alliance but during the course of the 1896–97 season was wound up, the final straw being an 8–1 home defeat to Royal Albert at Christmas.