The men's javelin throw event at the 2006 World Junior Championships in Athletics was held in Beijing, China, at Chaoyang Sports Centre on 16 and 19 August.
| Gold | John Oosthuizen | |
| Silver | Ari Mannio | |
| Bronze | Roman Avramenko |
19 August
| Rank | Name | Nationality | Attempts | Result | Notes | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | ||||||||
| align=left | align=left | 78.52 | 83.07 | 79.89 | 79.58 | x | x | 83.07 | |||||
| align=left | align=left | | 75.97 | 74.46 | 73.83 | 75.39 | 72.15 | 77.26 | 77.26 | ||||
| align=left | align=left | | 76.01 | x | 75.80 | 75.47 | 75.50 | 74.90 | 76.01 | ||||
| 4 | align=left | align=left | 75.64 | 73.68 | 75.39 | x | 71.35 | x | 75.64 | ||||
| 5 | align=left | align=left |  | 74.46 | 68.83 | 70.97 | 75.35 | x | 72.13 | 75.35 | |||
| 6 | align=left | align=left | 69.10 | 63.13 | 73.58 | 72.73 | x | x | 73.58 | ||||
| 7 | align=left | align=left | 68.83 | 71.66 | 73.13 | 71.39 | 71.20 | 69.68 | 73.13 | ||||
| 8 | align=left | align=left | 71.07 | 65.94 | 68.96 | 68.86 | 67.70 | 69.92 | 71.07 | ||||
| 9 | align=left | align=left | | 66.86 | 71.01 | x | 71.01 | ||||||
| 10 | align=left | align=left | 70.06 | x | 70.39 | 70.39 | |||||||
| 11 | align=left | align=left |  | 69.32 | x | 67.84 | 69.32 | ||||||
| 12 | align=left | align=left | x | 63.45 | 61.52 | 63.45 | |||||||
16 August
| Rank | Name | Nationality | Attempts | Result | Notes | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | ||||||||
| 1 | align=left | align=left | | 68.35 | x | 74.17 | 74.17 | Q | ||
| 2 | align=left | align=left | 65.69 | 73.03 | - | 73.03 | Q | |||
| 3 | align=left | align=left | 67.04 | 66.57 | 71.52 | 71.52 | Q | |||
| 4 | align=left | align=left | 67.21 | 67.94 | 69.62 | 69.62 | q | |||
| 5 | align=left | align=left | 65.73 | 64.31 | 69.58 | 69.58 | q | |||
| 6 | align=left | align=left |  | 63.47 | 66.62 | 69.20 | 69.20 | |||
| 7 | align=left | align=left |  | 62.75 | 68.12 | 66.88 | 68.12 | |||
| 8 | align=left | align=left |  | 67.84 | x | 66.23 | 67.84 | |||
| 9 | align=left | align=left | | 63.96 | 67.74 | 62.91 | 67.74 | |||
| 10 | align=left | align=left | 63.96 | 63.97 | 66.28 | 66.28 | ||||
| 11 | align=left | align=left | 65.61 | x | 64.09 | 65.61 | ||||
| 12 | align=left | align=left |  | 63.57 | x | 64.49 | 64.49 | |||
| 13 | align=left | align=left | 63.88 | 61.56 | x | 63.88 | ||||
| 14 | align=left | align=left | 59.58 | x | 63.75 | 63.75 | ||||
| 15 | align=left | align=left | 63.20 | 62.81 | x | 63.20 | ||||
| 16 | align=left | align=left | 55.31 | 61.92 | 62.62 | 62.62 | ||||
| 17 | align=left | align=left |  | 56.64 | 59.43 | 58.70 | 59.43 | |||
| 18 | align=left | align=left |  | 54.97 | 57.76 | x | 57.76 | |||
| Rank | Name | Nationality | Attempts | Result | Notes | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | ||||||||
| 1 | align=left | align=left | 78.42 | - | - | 78.42 | Q | |||
| 2 | align=left | align=left | 69.06 | 68.48 | 73.18 | 73.18 | Q | |||
| 3 | align=left | align=left | | 72.80 | - | - | 72.80 | Q | ||
| 4 | align=left | align=left | | 71.15 | - | - | 71.15 | Q | ||
| 5 | align=left | align=left | | 70.98 | - | - | 70.98 | Q | ||
| 6 | align=left | align=left | 70.55 | - | - | 70.55 | Q | |||
| 7 | align=left | align=left | | 69.60 | 68.28 | 69.78 | 69.78 | q | ||
| 8 | align=left | align=left | 68.87 | x | x | 68.87 | ||||
| 9 | align=left | align=left | | 63.81 | 66.30 | 61.17 | 66.30 | |||
| 10 | align=left | align=left |  | 63.49 | 63.57 | 66.16 | 66.16 | |||
| 11 | align=left | align=left | 65.31 | 65.42 | 65.62 | 65.62 | ||||
| 12 | align=left | align=left | 62.67 | 63.43 | 65.13 | 65.13 | ||||
| 13 | align=left | align=left |  | 62.07 | 58.18 | 60.15 | 62.07 | |||
| 14 | align=left | align=left |  | 55.63 | 61.05 | 60.96 | 61.05 | |||
| 15 | align=left | align=left |  | 55.67 | 56.73 | 57.77 | 57.77 | |||
| 16 | align=left | align=left | 54.55 | 55.86 | x | 55.86 | ||||
According to an unofficial count, 34 athletes from 26 countries participated in the event.