The women's 5000 metres event at the 1999 European Athletics U23 Championships was held in Göteborg, Sweden, at Ullevi on 31 July 1999.
| Gold | Katalin Szentgyörgyi | |
| Silver | Cristina Iloc | |
| Bronze | Olivera Jevtić |
31 July
| Rank | Name | Nationality | Time | Notes | |||
|---|---|---|---|---|---|---|---|
| align=left | align=left | | 15:18.80 | CR | |||
| align=left | align=left | | 15:22.64 | ||||
| align=left | align=left | 15:24.83 | |||||
| 4 | align=left | align=left | 15:43.22 | ||||
| 5 | align=left | align=left | | 15:45.15 | |||
| 6 | align=left | align=left | 15:49.99 | ||||
| 7 | align=left | align=left |  | 15:51.35 | |||
| 8 | align=left | align=left |  | 15:56.03 | |||
| 9 | align=left | align=left |  | 16:03.75 | |||
| 10 | align=left | align=left |  | 16:04.47 | |||
| 11 | align=left | align=left | | 16:11.67 | |||
| 12 | align=left | align=left | 16:14.32 | ||||
| 13 | align=left | align=left | | 16:23.10 | |||
| 14 | align=left | align=left |  | 16:25.54 | |||
| align=left | align=left | DNF | |||||
| align=left | align=left | | DNF |
According to an unofficial count, 16 athletes from 11 countries participated in the event.
(1) (3) (1) (1) (2) (2) (1)