The men's 5000 metres event at the 2016 IAAF World U20 Championships was held at Zdzisław Krzyszkowiak Stadium on 23 July.
| Gold | Selemon Barega | |
| Silver | Jamal Abdi Dirieh | |
| Bronze | Wesley Ladema |
| Standing records prior to the 2016 IAAF World U20 Championships in Athletics | |||||
|---|---|---|---|---|---|
| World Junior Record | 12:47.53 | Paris, France | 6 July 2012 | ||
| Championship Record | 13:08.57 | Bydgoszcz, Poland | 13 July 2008 | ||
| World Junior Leading | 13:02.49 | Shanghai, China | 14 May 2016 | ||
| Rank | Name | Nationality | Time | Note | |
|---|---|---|---|---|---|
| 13:21.21 | PB | ||||
| 13:21.50 | NU20R | ||||
| 13:23.34 | PB | ||||
| 13:28.41 | PB | ||||
| 13:31.09 | |||||
| 13:35.10 | SB | ||||
| 13:50.60 | |||||
| 13:51.40 | NU20R | ||||
| 13:52.01 | PB | ||||
| 10 | 13:55.07 | PB | |||
| 11 | 13:55.90 | NU20R | |||
| 12 | 13:58.30 | PB | |||
| 13 | 14:08.38 | ||||
| 14 | 14:15.22 | ||||
| 15 | 14:15.35 | ||||
| 16 | 14:15.89 | ||||
| 17 | 14:20.39 | PB | |||
| 18 | 14:21.22 | ||||
| 19 | 14:23.33 | PB | |||
| 20 | 14:27.70 | ||||
| 21 | 14:36.83 | ||||
| 22 | 14:38.67 | ||||
| 23 | 14:46.28 | PB | |||
| 24 | 14:48.82 | ||||
| 25 | Jack O'Leary | 14:50.67 | PB | ||