1998–99 EHF Women's Cup Winners' Cup

The 1998–99 EHF Women's Cup Winners' Cup was the 23rd edition of EHF's competition for women's handball national cup champions. It ran from October 3, 1998, to May 15, 1999.

Defending champion Bækkelagets SK won again the competition, beating Ferrobús Tortajada in the final. For the first time in the Cup Winners' Cup's history no team from the former Eastern Bloc or former Yugoslavia reached the final.