Penola Football Club claims to be able to trace its history as far back as 1865, but details of the club's early years are sketchy.
Since World War Two the club has competed in five different leagues and associations, and enjoyed premiership success in three of them. Arguably its greatest achievement was to win three consecutive flags in the powerful South East and Border Football League during the early 1950s. More recently, in 2001 the Southern Eagles broke an eleven year premiership drought by overcoming Mundulla by 25 points in the Kowree-Naracoorte-Tatiara Football League grand final. After losing the next season's grand final to the same opponent, they added a second KNTFL flag in 2003.
Since then, the closest they have come to capturing another flag was second place in 2007.