The 2024–25 LEN Challenger Cup was the 3rd edition of a water polo competition organised by European Aquatics.

The top 2 from every pool advances to the quarter-finals, followed by semi-finals and finals.

The seeding was decided by as follows: Carouge Natation EVK Zaibas KVP Novaky (H) Vitória Sport Clube Royal Dauphins Mouscronnois ZV De Zaan ASA Tel Aviv Cetus Espoo Clube Fluvial Portuense APOEL Nicosia GZC Donk AVK Slovan Olimpija Welsh Wanderers Sliema ASC (H) Hapoel Palram Zvulun Limassol NC Held in Sliema, Malta

The seeded and unseeded clubs consist of the teams that finished first and second in the previous round respectively.

The only restriction was that clubs from the same group in the previous round could not be drawn against each other.