Cowlairs was one of the clubs which together formed the Scottish League, but finished bottom of the table at the end of its first season, not helped by having four points deducted for fielding ineligible players.

Despite not being in any league competition the following season, the club enjoyed its longest Scottish Cup run, losing to Celtic in the quarter-finals.

Cowlairs' return to League football started well, securing runners-up spot that season to Hibernian; however, the club were not promoted to Division One, missing out following a ballot to third-placed Clyde.

They continued to be beset by financial and administrative problems, and after finishing bottom of Division Two in 1895–96, the club were again voted out of the league.

Petershill Juniors were formed in summer 1897, just after Northern folded and a year after Cowlairs; due to the circumstances they could be seen as a successor representing the Springburn area, albeit their club history does not mention either club, only linking their formation to the demise of St Mungo's Juniors in the area.