2016 AFF Championship knockout stage
The knockout stage was the second and final stage of the 2016 AFF Championship, following the group stage. It was played from 3 to 17 December with the top two teams from each group advanced to the knockout stage to compete in a single-elimination tournament. Each tie was played on a home-and-away two-legged basis. The away goals rule, extra time and penalty shoot-out were used to decide the winner if necessary.
Thailand won 3–2 on aggregate against Indonesia in the final to win their record fifth title.
The top two placed teams from each of the two groups advanced to the knockout stage. In Group A, Thailand secured the group's top spot with 9 points after defeating hosts Philippines 1–0 in their last match while Indonesia became the group's runners-up with 4 points after beating Singapore 2–1. Meanwhile, in Group B, Vietnam secured the top spot with 9 points after defeating Cambodia 2–1 in their last match while hosts Myanmar became the group's runners-up with 6 points after defeating Malaysia 1–0.
Schedule
The schedule of each round was as follows.
Bracket
Scores after extra time are indicated by, and penalty shoot-out are indicated by.
Semi-finals
First leg
| Statistics | Indonesia | Vietnam |
| Goals scored | 2 | 1 |
| Total shots | 13 | 11 |
| Shots on target | 6 | 3 |
| Ball possession | 40% | 60% |
| Corner kicks | 4 | 7 |
| Fouls committed | 10 | 15 |
| Offsides | 0 | 4 |
| Yellow cards | 1 | 2 |
| Red cards | 0 | 0 |
| Statistics | Myanmar | Thailand |
| Goals scored | 0 | 2 |
| Total shots | 9 | 16 |
| Shots on target | 5 | 9 |
| Ball possession | 35% | 65% |
| Corner kicks | 2 | 4 |
| Fouls committed | 18 | 7 |
| Offsides | 2 | 0 |
| Yellow cards | 2 | 1 |
| Red cards | 0 | 0 |
Second leg
Vietnam vs Indonesia
| Statistics | Vietnam | Indonesia |
| Goals scored | 2 | 2 |
| Total shots | 28 | 7 |
| Shots on target | 7 | 2 |
| Ball possession | 74% | 26% |
| Corner kicks | 13 | 3 |
| Fouls committed | 12 | 22 |
| Offsides | 2 | 4 |
| Yellow cards | 1 | 3 |
| Red cards | 1 | 0 |
Thailand vs Myanmar
| Statistics | Thailand | Myanmar |
| Goals scored | 4 | 0 |
| Total shots | 15 | 12 |
| Shots on target | 5 | 4 |
| Ball possession | 56% | 44% |
| Corner kicks | 5 | 3 |
| Fouls committed | 7 | 13 |
| Offsides | 2 | 1 |
| Yellow cards | 0 | 1 |
| Red cards | 0 | 0 |
Final
First leg: Indonesia vs Thailand
| Statistics | Indonesia | Thailand |
| Goals scored | 2 | 1 |
| Total shots | 11 | 11 |
| Shots on target | 4 | 3 |
| Ball possession | 39% | 61% |
| Corner kicks | 3 | 8 |
| Fouls committed | 16 | 10 |
| Offsides | 4 | 2 |
| Yellow cards | 0 | 0 |
| Red cards | 0 | 0 |
Second leg: Thailand vs Indonesia
| Statistics | Thailand | Indonesia |
| Goals scored | 2 | 0 |
| Total shots | 10 | 3 |
| Shots on target | 6 | 0 |
| Ball possession | 62% | 38% |
| Corner kicks | 6 | 2 |
| Fouls committed | 18 | 20 |
| Offsides | 2 | 1 |
| Yellow cards | 0 | 2 |
| Red cards | 0 | 1 |