The official Slovak Super Cup between the league champions and cup winners was decided in 13 matches actually played from 1994 through 2014. No match was staged in double-winning years, and the unofficial 1993 fixture against a league representative side is excluded. The competition was later discontinued and was replaced in 2017 by the separate cross-border Czech-Slovak Super Cup rather than another national edition.
| Season | Slovak Super Cup | Runner-up | Trophy |
|---|---|---|---|
| 2014 | ŠK Slovan Bratislava | MFK Košice Final: 1–0 |  |
| 2010 | MŠK Žilina | ŠK Slovan Bratislava Final: 1–1; won 4–2 on penalties | — |
| 2009 | ŠK Slovan Bratislava | MFK Košice Final: 2–0 | — |
| 2007 | MŠK Žilina | FC ViOn Zlaté Moravce Final: 1–1; won 5–4 on penalties | — |
| 2005 | Artmedia Bratislava | MFK Dukla Banská Bystrica Final: 3–1 | — |
| 2004 | MŠK Žilina | Artmedia Bratislava Final: 2–1 | — |
| 2003 | MŠK Žilina | FK Matador Púchov Final: 2–0 | — |
| 2002 | FK Koba Senec | MŠK Žilina Final: 1–1; won 4–3 on penalties | — |
| 1998 | FC Spartak Trnava | 1. FC Košice Final: 3–1 | — |
| 1997 | 1. FC Košice | ŠK Slovan Bratislava Final: 5–0 | — |
| 1996 | ŠK Slovan Bratislava | FC Chemlon Humenné Final: 3–1 | — |
| 1995 | Inter Bratislava | ŠK Slovan Bratislava Final: 3–2 | — |
| 1994 | ŠK Slovan Bratislava | FC TATRAN Prešov Final: 2–0 | — |
