Johnston, who joined Now from Emap's New Woman in April this year, is keeping details of the new project secret.
During her time as editor, Johnston oversaw the relaunch of the magazine in August, which was met with positive reviews.
She took over from Jane Ennis, the title's editor since its launch in 1996. Prior to this, Johnston held senior posts at New Woman, Bliss, Grazia, Marie Claire and Cosmopolitan.
She said: "I'd like to thank everyone in IPC for all the support they have given me whilst I have been here. I have loved my time at Now and wish the magazine and the team every success in the future."
Evelyn Webster, managing director of IPC Connect, and Andrew Sumner, the publishing director of Now, are now actively managing the recruitment process.
Webster said: "I'm sorry to be losing Helen, but pleased that she has agreed to stay on until Christmas. Undoubtedly, the editor's job on Now is one of the most hotly contested in UK journalism, and we're already in conversation with a number of very talented candidates to step in to the role."
The magazine's circulation has dropped by 8.5% year on year to 494,229 copies, according to the latest ABC figures for January to June this year.
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