The Channel 4 soap was honoured for its sensitive depiction of the gay love affair between Chester teenagers John-Paul McQueen (James Sutton) and Craig Dean (Guy Burnet).
Stonewall, an organisation that campaigns for equality for gay men and women, praised the show for its "sympathetic and convincing handling" of the "gritty and emotional" storyline.
Hollyoaks producer Bryan Kirkwood told DS: "I'm really chuffed that Hollyoaks has been recognised at the Stonewall Awards. It's a really prestigious award and one that means a lot the show, to James and Guy, to our writers and most importantly the audience that engaged with the story."
James Sutton added that he is "incredibly humbled" by the award, saying: "Stonewall is such an important organisation and it's amazing that we've been recognised by them for all the hard work we put into the storyline."