Gary Lockett last week stepped down from his post with immediate effect, citing his struggles to balance the demands of the job with his own business interests as the reason behind his resignation.
Lockett has remained as a non-executive director at Roots Hall but Kavanagh, former chief exec of Charlton who has worked in the game for over 10 years, has now taken the role of CEO.
Kavanagh told the club's official website: "I have known Ron Martin (chairman) for a number of years and I have seen first hand his passion and desire to deliver success for the club and I am looking forward to working along side Ron, and the rest of the board, to deliver what is a really exciting future.
"Part of this vision has to deliver success on the pitch and I will be working with Paul Sturrock to build on the feel-good factor that exists in the squad. I was at the match last night (Tuesday's 1-0 home defeat to Burton) and it ended disappointingly, but the spirit in the team having gone down to 10 men so early on, and the desire to go and win the game, was evident."
Kavanagh becomes Southend's third chief executive in the space of eight months following Lockett and Tara Brady, who also resigned from his post.