| Manager: | Keith Stevens and Alan McLeary (joint managers) |
| Stadium: | The New Den |
| League: | Division Two |
| League Result: | 5th (qualified for play-offs) |
| Cup1: | Play-offs |
| Cup1 Result: | Semi-finals |
| Cup2: | FA Cup |
| Cup2 Result: | First round |
| Cup3: | League Cup |
| Cup3 Result: | First round |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
During the 1999–2000 English football season, Millwall F.C. competed in the Football League Second Division, the third tier of English football.
Millwall had a good season and finished fifth in the Second Division, qualifying for the play-offs, but were beaten in the semi-finals by Wigan Athletic 1–0 on aggregate. The club also saw failure in both domestic cup competitions, being eliminated from both in the first round.