The men's 5000 metres event at the 2006 World Junior Championships in Athletics was held in Beijing, China, at Chaoyang Sports Centre on 20 August.
| Gold | Tariku Bekele | |
| Silver | Abreham Cherkos | |
| Bronze | Joseph Ebuya |
20 August
| Rank | Name | Nationality | Time | Notes | |||
|---|---|---|---|---|---|---|---|
| align=left | align=left | | 13:31.34 | ||||
| align=left | align=left | | 13:35.95 | ||||
| align=left | align=left | | 13:42.93 | ||||
| 4 | align=left | align=left | | 13:44.03 | |||
| 5 | align=left | align=left |  | 13:51.44 | |||
| 6 | align=left | align=left |  | 13:51.60 | |||
| 7 | align=left | align=left | 14:00.95 | ||||
| 8 | align=left | align=left |  | 14:06.86 | |||
| 9 | align=left | align=left |  | 14:12.69 | |||
| 10 | align=left | align=left |  | 14:15.10 | |||
| 11 | align=left | align=left |  | 14:15.54 | |||
| 12 | align=left | align=left | | 14:18.57 | |||
| 13 | align=left | align=left |  | 14:19.33 | |||
| 14 | align=left | align=left |  | 14:22.38 | |||
| 15 | align=left | align=left | | 14:23.50 | |||
| 16 | align=left | align=left | | 14:26.23 | |||
| 17 | align=left | align=left |  | 14:28.27 | |||
| 18 | align=left | align=left |  | 14:29.00 | |||
| 19 | align=left | align=left | | 14:30.83 | |||
| 20 | align=left | align=left | | 14:35.55 | |||
| 21 | align=left | align=left |  | 14:35.64 | |||
| 22 | align=left | align=left | 16:02.18 | ||||
| align=left | align=left | | DQ |
According to an unofficial count, 23 athletes from 15 countries participated in the event.