Dubke, 47, occupied the high-powered but low-profile, post for three crisis-filled months. "I can confirm that Dubke has resigned," an official told AFP.
No date for his departure, which has been in the works for almost two weeks, has been announced.
For months rumors have echoed around the West Wing about Trump being poised to fire his public relations staff en masse.
Many come from the Republican Party establishment and have been uneasy allies with the president.
Watch: Trump administration is preparing for a deeper investigation into its links with Russia
Trump has privately and publicly expressed fury over a litany of bad headlines, lashing out at reporters, alleged "fake news" headlines and staff.
The president's failure to pass significant legislation, legal challenges to his executive orders and a rolling scandal over his inner circle's ties with Russia have hobbled his young administration.
That has put the future of press secretary Sean Spicer and his staff into doubt.
Although the White House communications director is a much less recognizable figure than Spicer, they are usually major players -- defining how the West Wing communicates and shaping the media agenda.
During Barack Obama's administration top aide and confidant Dan Pfeiffer held the post.
