Lucy Allan will step into Bryan's shoes and will work alongside creative director Tony Wood and the newly-appointed head of production Ian Hopkins.
Allan joined the Hollyoaks team at its production house Lime Pictures as script assistant and quickly worked her way through the ranks to series script editor and deputy producer. She is currently heading up production of a new E4 Late Night Hollyoaks.
Speaking of her new position, she said: "This is an irresistible opportunity and I'm very excited by the challenge of taking on a show as successful as Hollyoaks.
"Having already worked with the talented production team and cast, I'm looking forward to developing new ideas and planning the show's future."
Lime Pictures creative director Tony Wood commented: "Bryan has created a legacy of success and award winning television which everyone at Lime Pictures is immensely proud of. Lucy’s signing reflects renewed ambition and confidence here during a thriving spell of output."
Kirkwood joined Hollyoaks in January 2006 after five years working on ITV soap Coronation Street as a storyliner. He was involved in iconic storylines such as Richard 'Tricky Dicky' Hillman's (Brian Capron) reign of terror over the Platts and Peter Barlow's (Chris Gascoyne) bigamy. He went on to become script editor at Corrie, before moving to Hollyoaks as producer.
His highlights with the Channel 4 soap include the fire at The Dog, Clare's (Gemma Bissix) manipulation of Max (Matt Littler) and Justin (Chris Fountain), Becca's (Ali Bastian) doomed love affair and most recently, 'Who Pushed Clare?' and Hannah's (Emma Rigby) anorexia. He won a legion on fans for his McDean storyline which saw John Paul McQueen (James Sutton) embark on a gay love affair with his best friend Craig Dean (Guy Burnet).
Earlier this year, Hollyoaks won more British Soap Awards than any other soap.
Kirkwood will remain with Hollyoaks until the end of the year, with his material running into the early part of 2009. Beyond his departure, he will maintain strong ties with Lime Pictures and continue to work with the company on potential new projects.