The club was formed in 1948 as 'Juventus' by Italian migrants from an amalgamation of several smaller clubs. Brunswick Juventus became the dominant side of Victorian football in the 1950s, winning six titles, including five consecutive titles from 1952–1956, and were arguably the club which ushered in the European migrant dominance of Victorian football, which remains to this day. In the 1960s while the club remained more than competitive, the rise of other migrant clubs, principally South Melbourne, saw this dominance ended, and the club would have to wait until 1970 to add to its trophy collection.
The club largely struggled in the league during the 1970s after their 1970 championship, though there were also four Dockerty Cup wins during this time. The club was not a foundation member of the National Soccer League (NSL) in 1977. In 1980 the club changed its name from Juventus to Brunswick United Juventus. When the NSL created the conference system in 1984, Brunswick finally joined the national league ranks, and after reaching the finals in their debut season, followed it up with their greatest achievement, the 1985 National Soccer League title, defeating Heidelberg, South Melbourne and Preston in the southern conference play-offs before eventually defeating Sydney City over two legs in the Grand Final.
1986 saw Brunswick finish first on the southern conference table, but consecutive losses to Adelaide City and Footscray JUST in the finals ended their season, and the last in which they were to be a force at national league level. An eighth place finish in 1987 was followed by a 13th place finish in 1988 and relegation to the state leagues where decent performances saw them win their eighth Victorian title in 1991.
Rejoining the NSL for the 1993/94 season as Brunswick Pumas and later Melbourne Zebras, the club struggled for two seasons before in 1996, it was demoted to the Victorian Premier League competition, Victoria's top men's senior division.
Between 1997 and 2011, the senior club, entered into a series of mergers and relocations, but have returned to Moreland, the municipality surrounding Brunswick, to become the Moreland Zebras in 2012. During this period, the senior team were Victorian Premier League runners up in 1997, Victorian Premier League Champions in 1998 as the Bulleen Inter Kings, and became 10th time champions of Victoria once again in 2004, playing as the Bulleen Zebras. The clubs relocation from Bulleen to the City of Whittlesea in 2007, saw the team finish Victorian Premier League runners up in 2007 as the Whittlesea Zebras. The club's latest and 11th Victorian championship title was celebrated in 2011, when it was crowned Victorian State League Division 1 champions as the Whittlesea Zebras, and promoted up to the Victorian Premier League as the Moreland Zebras.
The Moreland Zebras seniors will play its home games at Epping Stadium, on Harvest Home Road in Epping and its junior division currently occupy De Chene Reserve, in Coburg. The senior Zebras have played at Epping Stadium since 2007. It has a capacity of 10,000 and has hosted A league and some women international games.
In 2013 the Zebras will commence playing at a new soccer-specific field in the City of Moreland, Victoria.