According to Capital, Lyons has left to work in the new media sector although it is unclear whether he has a specific job lined up.
Lyons was responsible for all marketing at the station, including digital development and brand strategy during a time that saw him take responsibility for the launch of the 'Johnny Vaughan Breakfast Show'.
His resignation marks the third senior departure from Capital and its parent firm GCap, which was created from the merger of Capital and GWR two years ago.
Other top table departees were commercial director Linda Smith and chief executive David Mansfield.
Steve Orchard, GCap group operations director, said: "We are sad that Carl has decided to leave the station, he is a fantastic brand marketer and has done a great job since he was recruited to launch the 'Johnny Vaughan Breakfast Show'."
Prior to Capital, Lyons held a a number of marketing roles at companies such as Guinness, The Guardian and Lastminute.com, from where he joined Capital.
Lyons said: "I've had a fantastic three years at Capital and I am very proud that we've launched and established London's favourite breakfast show. I'm looking forward to pursuing options in the interactive space."
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