Allan, who succeeded incoming EastEnders producer Bryan Kirkwood, will vacate her office later this month to make way for former Bill exec and Footballers' Wives creator Paul Marquess.
She took office at Hollyoaks' home at Lime Pictures in Liverpool last January.
Since her appointment, Allan has overseen storylines which have included the teen soap's first ever non-linear week and the recent 'flashforward' instalment featuring Calvin's death.
Speaking of her decision to stand down, she said: "I am very proud to have been part of the Hollyoaks team. I've had a fantastic time working on this show but am now equally excited about what the future will hold."
Of his appointment, Marquess said: "Taking up this position at Lime Pictures feels like I'm going home, as I began my career working with both Carolyn and Tony at Granada and my first major project was Brookside at Mersey Television. I'm a huge soap fan so to be handed the reins of Channel 4's flagship teen drama is not only a huge challenge but also a massive honour."
Lime Pictures creative director and Hollyoaks exec producer Tony Wood added: "I'd like to thank Lucy Allan for making such a contribution to Hollyoaks over the years and wish her well for the future. It’s very exciting to be working with Paul Marquess again. He’s one of the best showrunners in the business. This is a brilliant appointment for Hollyoaks."
Allan is currently discussing other "new drama development opportunities" within Lime Pictures.