The men's 5000 metres event at the 1998 World Junior Championships in Athletics was held in Annecy, France, at Parc des Sports on 31 July and 2 August.
| Gold | Million Wolde | |
| Silver | Kipchumba Mitei | |
| Bronze | Reuben Kamzee |
2 August
| Rank | Name | Nationality | Time | Notes | ||||
|---|---|---|---|---|---|---|---|---|
| align=left | align=left | | 13:47.49 | |||||
| align=left | align=left | | 13:49.60 | |||||
| align=left | align=left | | 13:51.22 | |||||
| 4 | align=left | align=left |  | 14:06.24 | ||||
| 5 | align=left | align=left | | 14:06.30 | ||||
| 6 | align=left | align=left |  | 14:06.63 | ||||
| 7 | align=left | align=left |  | 14:06.83 | ||||
| 8 | align=left | align=left |  | 14:07.65 | ||||
| 9 | align=left | align=left |  | 14:07.77 | ||||
| 10 | align=left | align=left | | 14:09.64 | ||||
| 11 | align=left | align=left | 14:15.90 | |||||
| 12 | align=left | align=left | 14:19.50 | |||||
| 13 | align=left | align=left | 14:32.66 | |||||
| 14 | align=left | align=left |  | 14:34.32 | ||||
| align=left | align=left | | bgcolor=pink | DQ | IAAF rule 141 |
31 July
| Rank | Name | Nationality | Time | Notes | |||
|---|---|---|---|---|---|---|---|
| 1 | align=left | align=left | | 14:07.50 | Q | ||
| 2 | align=left | align=left | | 14:07.61 | Q | ||
| 3 | align=left | align=left | | 14:07.80 | Q | ||
| 4 | align=left | align=left | | 14:09.12 | Q | ||
| 5 | align=left | align=left | | 14:09.24 | Q | ||
| 6 | align=left | align=left | | 14:09.57 | q | ||
| 7 | align=left | align=left | | 14:22.47 | q | ||
| 8 | align=left | align=left | | 14:27.13 | q | ||
| 9 | align=left | align=left | 14:27.95 | q | |||
| 10 | align=left | align=left | 14:28.94 | ||||
| 11 | align=left | align=left | | 14:54.74 | |||
| 12 | align=left | align=left | 14:56.82 | ||||
| 13 | align=left | align=left | 15:08.92 | ||||
| 14 | align=left | align=left |  | 15:30.97 |
| Rank | Name | Nationality | Time | Notes | ||||
|---|---|---|---|---|---|---|---|---|
| 1 | align=left | align=left | | 14:25.00 | Q | |||
| 2 | align=left | align=left | | 14:25.14 | Q | |||
| 3 | align=left | align=left | 14:26.62 | Q | ||||
| 4 | align=left | align=left | 14:27.05 | Q | ||||
| 5 | align=left | align=left | | 14:27.62 | q | |||
| 6 | align=left | align=left |  | 14:28.54 | ||||
| 7 | align=left | align=left | 14:56.98 | |||||
| 8 | align=left | align=left |  | 15:01.91 | ||||
| 9 | align=left | align=left |  | 15:07.43 | ||||
| 10 | align=left | align=left | | 15:10.32 | ||||
| 11 | align=left | align=left | 15:15.29 | |||||
| 12 | align=left | align=left |  | 15:44.96 | ||||
| align=left | align=left | | bgcolor=pink | DQ | IAAF rule 141 Q |
According to an unofficial count, 27 athletes from 20 countries participated in the event.