The men's 5000 metres event at the 2009 European Athletics U23 Championships was held in Kaunas, Lithuania, at S. Dariaus ir S. Girėno stadionas (Darius and Girėnas Stadium) on 16 July.
| Gold | Mohamed Elbendir | |
| Silver | Noureddine Smaïl | |
| Bronze | David McCarthy |
16 July
| Rank | Name | Nationality | Time | Notes | |||
|---|---|---|---|---|---|---|---|
| align=left | align=left | | 13:55.10 | ||||
| align=left | align=left | | 13:59.23 | ||||
| align=left | align=left | | 14:00.78 | ||||
| 4 | align=left | align=left | 14:03.87 | ||||
| 5 | align=left | align=left | 14:04.15 | ||||
| 6 | align=left | align=left |  | 14:04.79 | |||
| 7 | align=left | align=left |  | 14:07.62 | |||
| 8 | align=left | align=left | 14:09.13 | ||||
| 9 | align=left | align=left |  | 14:10.10 | |||
| 10 | align=left | align=left | 14:11.44 | ||||
| 11 | align=left | align=left | | 14:12.70 | |||
| 12 | align=left | align=left |  | 14:13.85 | |||
| 13 | align=left | align=left | 14:15.00 | ||||
| 14 | align=left | align=left | 14:19.52 | ||||
| 15 | align=left | align=left |  | 14:21.18 | |||
| 16 | align=left | align=left | | 14:21.76 | |||
| 17 | align=left | align=left |  | 14:25.83 | |||
| 18 | align=left | align=left | | 14:31.44 | |||
| 19 | align=left | align=left | 14:32.51 | ||||
| 20 | align=left | align=left | | 15:16.45 |
According to an unofficial count, 20 athletes from 12 countries participated in the event.
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