In season 2013, Northcote City won their first Victorian Premier League Championship, defeating Bentleigh Greens SC 3–2 after extra time at AAMI Park.

A milestone in the club's history was moving to John Cain Memorial Park in 1979, which even today is considered one of the state's best soccer venues.

The club first gained promotion into the Victorian Soccer Federation leagues in 1964 after competing in the amateur competitions in its formative years.

The 1990s were not much kinder when a Victorian Soccer Federation restructure in 1999 saw the club relegated to State League Division 2 despite finishing 5 places form the bottom of the ladder.

In their first year back in the Victorian Premier League, Northcote City finished 5th on 31 points, qualifying for the Elimination Final which they lost 3–1 to Heidelberg United.

Despite failing to reach the finals, they did manage to end the season with some silverware, defeating Melbourne Knights FC 2–0 at AAMI Park to lift the Mirabella Cup.

Northcote City enjoyed the most successful season in its history in 2013, the same year a stalwart and life member of the club, Emmanuel Himonas died, winning the minor premiership in the Victorian Premier League, followed by winning the VPL Grand Final against Bentleigh Greens 3–2.

[5] In April 2016, Northcote announced the return of former head coach and VPL winner Goran Lozanovski as Gymnopoulos' replacement.

[6] Lozanovski signed eleven players in the mid-season transfer window, including former Newcastle Jets FC striker Braedyn Crowley.