Bohemians will play Scottish League 1 side Airdrie in the third round of the Tunnock's Caramel Wafer Scottish Challenge Cup.
Waterford will play Hearts Under-20s at the RSC.
The League of Ireland duo are part of 32 teams which features clubs from Scotland, Wales, England and Northern Ireland.
The ties will be played on the weekend of 7/8 September.
Bohs reached the quarter-finals last year but withdrew after the game at Dalymount Park with East Fife was postponed due to a frozen pitch.