| Club: | Croatia Zagreb |
| Season: | 1998–99 |
| Manager: | Zlatko Kranjčar (until October) Velimir Zajec (from October) |
| Stadium: | Stadion Maksimir |
| League: | Prva HNL |
| League Result: | 1st |
| Cup1: | Croatian Cup |
| Cup1 Result: | First round |
| Cup2: | Champions League |
| Cup2 Result: | Group stage |
| League Topscorer: | Edin Mujčin (10) |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
During the 1998–99 Croatian football season, Croatia Zagreb competed in the Prva HNL.
Croatia Zagreb made their debut in the Champions League group stage, drawn against Olympiakos, Porto and Ajax. Zagreb failed to win any of their first three group games, resulting in the departure of manager Zlatko Kranjčar. His replacement, Velimir Zajec, inspired a turnaround and wins against Porto and Ajax gave the club hope of reaching the quarter-finals. A home draw with Olympiakos in the final group stage match saw Croatia Zagreb finish second in their group, but as they were the lowest-ranked of all the group stage runners-up they did not progress.
Squad at end of season[1]