| 2. Round | 28/08/2016 | FC Edmonton | - | Puerto Rico FC | 0:0 | ||||
| 3. Round | 04/09/2016 | Puerto Rico FC | - | Miami FC | 0:3 | ||||
| 3. Round | 08/09/2016 | Puerto Rico FC | - | Ottawa Fury | 0:0 | ||||
| 3. Round | 11/09/2016 | Tampa Bay Rowdies | - | Puerto Rico FC | 0:0 | ||||
| 3. Round | 18/09/2016 | Puerto Rico FC | - | Jacksonville Armada | 3:3 | ||||
| 3. Round | 24/09/2016 | Miami FC | - | Puerto Rico FC | 0:1 | ||||
| 3. Round | 29/09/2016 | Puerto Rico FC | - | Fort Lauderdale Strikers | 2:1 | ||||
| 4. Round | 02/10/2016 | Ottawa Fury | - | Puerto Rico FC | 1:2 |  |
|||
| 4. Round | 09/10/2016 | Puerto Rico FC | - | Minnesota United FC | 0:0 | ||||
| 4. Round | 16/10/2016 | Fort Lauderdale Strikers | - | Puerto Rico FC | 2:0 | ||||
| 4. Round | 23/10/2016 | Indy Eleven | - | Puerto Rico FC | 3:0 | ||||
| 4. Round | 30/10/2016 | Puerto Rico FC | - | Carolina RailHawks | 2:1 |
USA