The men's 5000 metres event at the 1986 World Junior Championships in Athletics was held in Athens, Greece, at Olympic Stadium on 17 and 19 July.
| Gold | Peter Chumba | |
| Silver | Alejandro Gómez | |
| Bronze | Melese Feissa |
19 July
| Rank | Name | Nationality | Time | Notes | |||
|---|---|---|---|---|---|---|---|
| align=left | align=left | | 13:55.25 | ||||
| align=left | align=left | | 13:55.94 | ||||
| align=left | align=left | | 13:56.45 | ||||
| 4 | align=left | align=left |  | 13:57.48 | |||
| 5 | align=left | align=left | 13:57.49 | ||||
| 6 | align=left | align=left | | 13:59.51 | |||
| 7 | align=left | align=left | | 14:00.36 | |||
| 8 | align=left | align=left |  | 14:00.46 | |||
| 9 | align=left | align=left |  | 14:01.40 | |||
| 10 | align=left | align=left | 14:08.68 | ||||
| 11 | align=left | align=left |  | 14:09.51 | |||
| 12 | align=left | align=left | 14:12.35 | ||||
| 13 | align=left | align=left |  | 14:15.84 | |||
| 14 | align=left | align=left | | 14:20.03 | |||
| 15 | align=left | align=left | | 14:28.08 | |||
| 16 | align=left | align=left |  | 14:34.09 | |||
| 17 | align=left | align=left |  | 14:34.28 | |||
| 18 | align=left | align=left | 14:34.50 |
17 July
| Rank | Name | Nationality | Time | Notes | |||
|---|---|---|---|---|---|---|---|
| 1 | align=left | align=left | | 13:59.52 | Q | ||
| 2 | align=left | align=left | | 14:01.44 | Q | ||
| 3 | align=left | align=left | | 14:02.05 | Q | ||
| 4 | align=left | align=left | | 14:06.42 | Q | ||
| 5 | align=left | align=left | | 14:06.58 | Q | ||
| 6 | align=left | align=left | 14:09.79 | Q | |||
| 7 | align=left | align=left | | 14:15.38 | q | ||
| 8 | align=left | align=left | 14:20.12 | q | |||
| 9 | align=left | align=left | | 14:22.31 | |||
| 10 | align=left | align=left | 14:35.27 | ||||
| 11 | align=left | align=left | 14:41.84 | ||||
| 12 | align=left | align=left |  | 14:53.01 | |||
| 13 | align=left | align=left | 14:58.14 | ||||
| 14 | align=left | align=left |  | 15:06.14 | |||
| 15 | align=left | align=left |  | 15:16.39 | |||
| 16 | align=left | align=left | 15:49.00 | ||||
| 17 | align=left | align=left | 15:54.89 | ||||
| 18 | align=left | align=left | 16:04.79 |
| Rank | Name | Nationality | Time | Notes | |||
|---|---|---|---|---|---|---|---|
| 1 | align=left | align=left | | 14:11.30 | Q | ||
| 2 | align=left | align=left | | 14:11.83 | Q | ||
| 3 | align=left | align=left | 14:12.42 | Q | |||
| 4 | align=left | align=left | | 14:13.18 | Q | ||
| 5 | align=left | align=left | | 14:15.43 | Q | ||
| 6 | align=left | align=left | | 14:15.99 | Q | ||
| 7 | align=left | align=left | | 14:17.34 | q | ||
| 8 | align=left | align=left | | 14:17.88 | q | ||
| 9 | align=left | align=left | 14:18.62 | q | |||
| 10 | align=left | align=left | | 14:19.25 | q | ||
| 11 | align=left | align=left |  | 14:24.49 | |||
| 12 | align=left | align=left |  | 14:27.61 | |||
| 13 | align=left | align=left | 14:27.62 | ||||
| 14 | align=left | align=left |  | 15:00.35 | |||
| 15 | align=left | align=left | | 15:12.99 | |||
| 16 | align=left | align=left | 15:17.85 | ||||
| 17 | align=left | align=left |  | 15:20.31 | |||
| 18 | align=left | align=left | 16:14.17 | ||||
| 19 | align=left | align=left |  | 16:40.60 |
According to an unofficial count, 37 athletes from 30 countries participated in the event.