| Champ: |  Mitchell Krueger Daniel Nguyen |
| Runner: |  Jarryd Chaplin Benjamin Mitchell |
| Score: | 6–2, 7–5 |
| Edition: | 1st |
| After Name: | Winnipeg National Bank Challenger – Men's doubles |
| Main Name: | Winnipeg Challenger |
See main article: article and 2016 Winnipeg National Bank Challenger.
This was the first edition of the men's doubles tournament.
Mitchell Krueger and Daniel Nguyen won the title, defeating Jarryd Chaplin and Benjamin Mitchell 6–2, 7–5 in the final.
The top two seeds receive a bye into the quarterfinals.