Gibson will be responsible for day-to-day editing of the site content, reporting to director of digital content and editor in chief Alan Rushbridger.
Emily Bell, who was informally in charge of editing the website, will focus on her role as director of digital content and continue to lead the site's strategic direction.
Bell said: "I'm delighted with this appointment. Janine brings a wealth of experience in print and online to this new role and working with our editorial team she will continue to build on our position as the UK's most popular newspaper website."
Gibson began her career in trade magazines, first on Televisual, a monthly magazine for independent producers and then on television industry weekly Broadcast where she was international editor.
She was media correspondent of the Independent before moving to the same role at the Guardian in 1998. Gibson became media editor of the Guardian and was the launch editor of Mediaguardian.co.uk.
For the past 18 months she has also undertaken the role of executive editor of Guardian.co.uk.
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