On 22 March 2018, Bowyer was named caretaker manager of Charlton Athletic after former manager Karl Robinson left by mutual consent. His managerial career began with a 2–0 win two days later against Plymouth Argyle After winning his first three games, in April he was given the role until the end of the season. His spell in charge ended on 13 May after Charlton were beaten 2–0 on aggregate by Shrewsbury Town in the League One play-off semi final. On 14 June, Bowyer was renamed caretaker manager until further notice, and on 6 September, his role was made permanent on a contract lasting until the end of the season.