The 1999-2000 Slovenian Cup was won by HK Olimpija Ljubljana, who defeated HK Acroni Jesenice in the final. The first round of the cup was played from November 4, 1999, to January 20, 2000. The top two teams qualified for the final tournament, which was held from September 2-3, 2000. HK Olimpija Ljubljana and HK Jesenice joined the competition for the final round.