The 1998–99 FIBA Saporta Cup was the thirty-third edition of FIBA's 2nd-tier level European-wide professional club basketball competition.

For the 1998–1999 FIBA Saporta Cup, the countries are allocated places according to their place on the FIBA country rankings, which takes into account their performance in European competitions from 1995–96 to 1997–98.

[1] The labels in the parentheses show how each team qualified for the place of its starting round: *The second leg which was scheduled to be played in Podgorica, was cancelled due to the war situation in Yugoslavia.

Although FIBA accepted a neutral venue (Thessaloniki, Greece) to play this game, the Yugoslav players couldn't get out of their country because of the military conflict, and therefore FIBA definitely cancelled this match and awarded a forfeit (20–0) to Benetton Treviso.

April 13, Pabellón Príncipe Felipe, Zaragoza