The executive editor and senior vice president will end her work on the DC Comics imprint, which began with its founding in 1993.
Berger has worked for DC for 33 years, in which time she has overseen some of its most successful publications including Neil Gaiman's Sandman, Hellblazer, Fables, Preacher, 100 Bullets, Y: The Last Man and American Vampire.
"I've been incredibly proud to have provided a home where writers and artists could create progressive and provocative stories that broadened the scope of comics, attracting a new and diverse readership to graphic storytelling," said Berger in a statement.
"I'd like to thank all the many immensely talented creators who have helped make Vertigo into a daring and distinctive imprint and I'm grateful to everyone at DC Entertainment and the retail community for their support and commitment to Vertigo all these years.
"It's been quite an honour."
Berger will continue at Vertigo until March 2013, "assisting in the transition to a new leadership team".
The news comes at a time of uncertainty for the imprint, which has seemingly ceased publishing new series or graphic novels.
With the cancellation of Hellblazer (which will restart under the mainstream DC banner as Constantine) and the hiatus of American Vampire, Fables remains its most successful and long-running title.