| 1. Round | 03/07/2016 | Puerto Rico FC | - | Indy Eleven | 1:1 | ||||
| 1. Round | 10/07/2016 | Jacksonville Armada | - | Puerto Rico FC | 2:1 | ||||
| 1. Round | 14/07/2016 | Rayo OKC | - | Puerto Rico FC | 2:2 | ||||
| 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 | ||||
| 2. Round | 14/08/2016 | Carolina RailHawks | - | Puerto Rico FC | 2:2 | ||||
| 2. Round | 21/08/2016 | Puerto Rico FC | - | New York Cosmos | 1:2 | ||||
| 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 |  |
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| 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 |  |
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| 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 |
Puerto Rico