Honan, who was assistant editor on the Saturday edition under Sarah Sands, is understood to be leaving the title on amicable terms, but her high-profile departure comes amid a wave of fresh job cuts at the Telegraph Group.
Meanwhile, the NUJ is planning to submit notice of an intended strike ballot in response to the 133 compulsory redundancies expected at the Telegraph Group, which are part of the company's multimillion-pound online and print integration programme.
The NUJ has confirmed that three foreign correspondents have had their contracts terminated at the Telegraph, sparking speculation that major job cuts are imminent.
John Carey, the Telegraph's NUJ father of chapel, said: "They're tearing the heart out of this paper and each day that goes by they are doing it more and more."
Jeremy Dear, general secretary of the NUJ, said: "This is a dispute about protecting both the rights of those who work for the Telegraph and most importantly about protecting the future of the paper.
"The company's plans simply won't work and are set to damage the quality journalism, which is the basis on which the future success of the group depends."
There is no suggestion that Honan's departure is directly part of the expected job cuts.
Honan's most recent roles at the Telegraph include planning book serialisation deals, News Review and political interviews for the Saturday edition.
She said: "I have had a wonderful time at the Telegraph. I wish John Bryant and his team all the best."
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