| Season: | 1999–2000 |
| Winners: | Maccabi Petah Tikva (2nd title) |
| Nextseason: | 2000–01 |
The 1999–2000 Toto Cup Al was the 16th season of the third-most important football tournament in Israel since its introduction. This was the first edition to be played with both Israeli Premier League and Liga Leumit clubs.
The competition began on 6 August 1999 and ended on 15 February 2000, with Maccabi Petah Tikva beating Maccabi Haifa 4–1 in the final.
Starting with this edition, the competition was played as a knock-out tournament, with the first two rounds played over two legs, with ties from the quarter-finals and on were decided in a single match.
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