Epona's Song is learned from Malon at Lon Lon Ranch when Link is a child. Malon learned the song from her mother, and during daytime (as well as during their previous encounter near Hyrule Castle) Malon can be heard singing the song. As they learn the song, the usually shy and easily frightened young filly Epona approaches Link and acts calmly around him, as the song has a calming effect on her.

Later, when Link returns to the ranch as an adult, the ranch has been taken over by Ingo, who has been corrupted by evil. Ingo allows Link to ride his horses inside the pen for a small amount of time, for a price of 10 Rupees. Link plays "Epona's Song," calling Epona to him. Ingo challenges Link to a horse race around the pen. Link wins the first round, and Ingo is outraged. Not noticing what horse Link is riding, he wagers the ownership of Epona to the winner of the next race. Ingo is beaten again, and holds true to his word — however, he notices that the horse is Epona, whom he could not tame, and seal the two inside his ranch. Epona and Link escape the ranch by jumping over the fences. Subsequently, Link can play "Epona's Song" while in the overworld to call Epona to him and ride her.