Glen Waverley made its first known grand final in 1928, defeating Dandenong Rovers. However, the match was replayed on protest, with the Rovers winning that game by 11 points, claiming the BDFA premiership.[3]
In 1961, the club joined the newly-formed Division 2 in the Victorian Football Association (VFA). They changed their name to Waverley to better reflect their representation of the region, and adopted the "Panthers" nickname in 1963.[5] They started strongly, winning half of their 18 matches that year, and then in 1963 finished runners up to Preston at Toorak Park. The club was promoted at short notice to the 1st Division in 1964 to fill the spot left after Moorabbin was suspended from the Association.[6] In its first season in Division 1, the club survived relegation back to Division 2 by winning the last game of the season against their nemesis from the previous season, Preston.[7]
The club's breakthrough year came in 1965 under the coaching of Ian Thorogood when, despite competing in just their second season in the top division, they claimed the premiership with a 12-point victory over Port Melbourne in the Grand Final at Port Melbourne's home ground. The following season they met again in the decider, but this time Port Melbourne was too strong. In 1970 they finished third, but in 1972 the club finished last and was relegated to Division 2, ending its nine-year stint in the top division.[8]
The club struggled for support in Division 2, and was also hindered by the opening of VFL Park in nearby Mulgrave, as many locals preferred to watch the VFL game played at the ground every Saturday than watch the Panthers on a Sunday.[9] In the mid-1970s when Association-wide crowds were averaging more than 4,500, Waverley still seldom drew more than 1,000 fans to games.[10] The club was runner-up in Division 2 in 1981, and earned promotion to the expanded 12-team Division 1 for 1982,[11] but returned to Division 2 in 1984 after two wooden spoons at the top level.[12] Waverley was Division 2 runner-up in its final season, 1987, then abruptly folded one month before the 1988 season due to financial difficulties.[13]
Under the new name of Waverley Amateurs, the club entered the VAFA's F Section for the 1989 season.[15]
In 1991, the club moved to the Eastern District Football League (EDFL) and reverted back to the "Waverley Football Club" name. The club was runners-up in the Division 4 grand finals in 1996 and 1997, while the EDFL became the Eastern Football League (EFL) at the end of the 1997 season.[2][16]
During the 1998 season (the EDFL became the Eastern Football League (EFL) at the end of the 1997 season)[18] the committees of Waverley and Mount Waverley Burwood discussed the possibility of merging to create a larger club that represented the Waverley district of the City of Monash. The merger was agreed on, and the new club − known as the Waverley Blues − entered the EFL in 1999.[19]