Source: [citation needed] As the Slovak First Football League champions, Slovan entered the competition in the first qualifying round.

The first qualifying round draw was held on 18 June 2024, Slovan were drawn against Macedonian First Football League champions Struga.

[1] The second qualifying round draw was held on 19 June 2024, Slovan were drawn against Slovenian PrvaLiga champions Celje.

[2] The third qualifying round draw was held on 22 July 2024, Slovan were drawn against Cypriot First Division champions APOEL.

[3] The play-off round draw was held on 5 August 2024, Slovan were drawn against Danish Superliga champions Midtjylland.