The actor, who plays bad boy Brendan Brady, will make an on-screen exit in March after two and a half years with the Channel 4 show.
Announcing the news and thanking his supporters, Scanlan commented: "To the greatest fans I could ever wish for - the time has come for me to sign out of Hollyoaks, to bow out as Double B.
"It has been the greatest honour to share the stage with you and I could think of no better company to spend my evenings with. Thank you for your love and loyalty and please, let's dance again another time, another role."
He added: "To the channel and Lime Pictures, thank you. A success built on surrounding myself with people who are better than me in every department, thank you."
Meanwhile, Hollyoaks' executive producer Bryan Kirkwood said: "In Brendan Brady, Emmett has created one of the most outstanding and memorable characters in Hollyoaks' 17-year history. The character has served the show incredibly well but after two action-packed, tear-stained years, we're very sad to say goodbye.
"Emmett's unique presence, both on screen and off, will be sorely missed by everyone at Hollyoaks, but we look forward to working with him on other Lime projects."
Scanlan first hinted that Brendan's story was drawing to a close late last year, but today (January 9) is the first time that his departure has been officially confirmed.
While little is known about how Brendan leaves, Digital Spy has learned that show bosses want him to go out with a bang in a dramatic final storyline.
Viewers will have to wait and see whether Brendan is killed off, makes a sudden escape from troubles in the village, or heads to prison as punishment for his past crimes.
Scanlan joined Hollyoaks in 2010 and has since established Brendan as one of the most popular characters in the show's history.
Brendan's major storylines have included his domestic violence and subsequent love story with Ste Hay (Kieron Richardson), explosive feuds with Warren Fox and Simon Walker, and disturbing encounters with his abusive father Seamus (Fintan McKeown).
Away from Hollyoaks, Scanlan has expressed an interest in working with Lime Pictures again on other projects, and is already being linked to another drama currently in development by the production firm.
Hollyoaks airs weeknights at 6.30pm on Channel 4, with first look screenings at 7pm on E4. Get the Inside Soap magazine on your iPhone or iPad