| 1999–2000 LEN Champions League | |
| League: | LEN Champions League |
| Sport: | Water Polo |
| Duration: | 27 October 1999 to 27 May 2000 |
| No Of Teams: | 8 (preliminary round) 28 (total) |
| Playoffs: | Final Four |
| Playoffs Link: | 1999–2000 LEN Champions League#Final Four (Bečej) |
| Finals Champ: | Bečej (1st title) |
| Seasonslist: | LEN Champions League |
| Seasonslistnames: | Champions League |
| Prevseason Link: | 1998–99 LEN Champions League |
| Prevseason Year: | 1998–99 |
| Nextseason Link: | 2000–01 LEN Champions League |
| Nextseason Year: | 2000–01 |
The 1999–2000 LEN Champions League was the 37th edition of LEN's premier competition for men's water polo clubs. It ran from 27 October 1999 to 27 May 2000, and it was contested by 28 teams. The Final Four (semifinals, final, and third place game) took place on May 26 and May 27 in Bečej.
| width=25 | ! | width=220 | Team |
|---|---|---|---|
| Bečej | |||
| HAVK Mladost | |||
 BVSC | |||
| POŠK |
| Aleksandar Šoštar, Predrag Zimonjić, Slobodan Soro, Goran Krstonošić, Nenad Vukanić, Branko Peković, Aleksandar Ćirić, Veljko Uskoković, László Tóth, Aleksandar Šapić, Jugoslav Vasović, Balázs Vincze, Nebojša Milić | |
| Head coach | |
| Zoltán Kásás |