Harry Whittaker - who had Down's syndrome - was honoured at the end of the episode on UTV with a photo captioned: "To Harry, With Love."
A spokesperson for Emmerdale said: "Very sadly we can confirm Harry Whittaker's passing last Tuesday 1st July. We will all miss him greatly and have offered our sincerest condolences to his family at this very sad time."
The cause of death has not yet been announced.
Following the episode, actor Mark Charnock, who plays Marlon, wrote on his Twitter page: "Our superhero. We were lucky to know you and hear your laugh. You lit up our lives, dearest, loveliest Harry."
After an outpouring of messages of condolence from fans, Charnock wrote: "Thank you all. We'll all pass on your overwhelming response to Harry's amazing family. Thank you for all your kind words. It means a lot. Xx"
The character of Leo made his first appearance in Emmerdale in May 2011.
He has also been played by another young child, Theo Tasker.