The men's 5000 metres event at the 1999 European Athletics U23 Championships was held in Göteborg, Sweden, at Ullevi on 1 August 1999.
| Gold | Youssef El Nasri | |
| Silver | Marius Bakken | |
| Bronze | Marco Mazza |
1 August
| Rank | Name | Nationality | Time | Notes | |||
|---|---|---|---|---|---|---|---|
| align=left | align=left | | 13:30.48 | CR | |||
| align=left | align=left | | 13:31.53 | ||||
| align=left | align=left | | 13:47.17 | ||||
| 4 | align=left | align=left |  | 13:53.12 | |||
| 5 | align=left | align=left | 13:56.87 | ||||
| 6 | align=left | align=left |  | 13:57.51 | |||
| 7 | align=left | align=left |  | 13:59.48 | |||
| 8 | align=left | align=left |  | 13:59.55 | |||
| 9 | align=left | align=left | 14:01.41 | ||||
| 10 | align=left | align=left | | 14:08.36 | |||
| 11 | align=left | align=left | | 14:19.53 | |||
| 12 | align=left | align=left | 14:19.68 | ||||
| 13 | align=left | align=left | 14:21.22 | ||||
| 14 | align=left | align=left | | 14:22.37 | |||
| align=left | align=left | | DNF | ||||
| align=left | align=left |  | DNF | ||||
| align=left | align=left | | DNF | ||||
| align=left | align=left | | DNF | ||||
| align=left | align=left | | DNF |
According to an unofficial count, 19 athletes from 10 countries participated in the event.
(2) (3) (2) (1) (1) (2) (3) (1)