The East Gippsland FL in its present incarnation began in 1974 with the merger of the Gippsland Football League and the Bairnsdale District Football League. The league has had a number of clubs fold, merge, leave and return over its history, due partly to changing economic circumstances in the area, with areas such as Orbost losing large amounts of their population.
At one stage in the 1980s, the league divided its clubs into two divisions, due to a desire to avoid weekly 40-goal drubbings for the weaker clubs. In 1984 the league had two divisions of five clubs each, both divisions having a club with a bye every week, this move enabling the league to save costs on umpiring.
However, in 1985 Wy Yung got promoted to first division, so the league then had six and four. The second division broke away in 1986 to form the Riviera Football League, together with some clubs who had left the North Gippsland Football League. After the Riviera FL disbanded in 2004, Paynesville was the only East Gippsland member club to return to the EGFL, with West Bairnsdale having folded in the interim, and Lindenow South and Swan Reach instead opting to join the Omeo & District Football League.
In 2011, the league dropped back to six clubs, with Bairnsdale returning to the Gippsland Football League. In 2012 season the league grew to again feature 7 clubs, with Stratford announcing that they would leave the North Gippsland Football League and join the EGFL. Boisdale-Briagolong followed suit in 2015, bringing the league to eight clubs.