| 1. Round | 17/07/2016 | Tampa Bay Rowdies | - | Puerto Rico FC | 3:0 | ||||
| 1. Round | 24/07/2016 | Puerto Rico FC | - | Rayo OKC | 1:0 | ||||
| 1. Round | 31/07/2016 | New York Cosmos | - | Puerto Rico FC | 3:0 |  |
|||
| 2. Round | 04/08/2016 | Minnesota United FC | - | Puerto Rico FC | 1:1 | ||||
| 2. Round | 07/08/2016 | Puerto Rico FC | - | FC Edmonton | 0:1 | ||||
| 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 | 29/09/2016 | Puerto Rico FC | - | Fort Lauderdale Strikers | 2:1 | ||||
| 4. Round | 16/10/2016 | Fort Lauderdale Strikers | - | Puerto Rico FC | 2:0 |
Puerto Rico