The 1999–2000 season was Birmingham City Football Club's 97th in the Football League. They finished in fifth place in the Football League First Division, qualifying for the promotion play-offs, but lost the first leg of the semifinal 4–0 at home to Barnsley. Although they won the away leg, they were eliminated 5–2 on aggregate. Birmingham entered the 1999–2000 FA Cup at the third round and lost to Everton in the fourth, and after entering the League Cup in the first round and defeating Newcastle United in the third, lost to West Ham United in the fourth round.
Paul Furlong was top scorer with 11 goals, all scored in league competition.