The Men's 50 metre butterfly S6 event at the 2016 Paralympic Games took place on 9 September 2016, at the Olympic Aquatics Stadium.

Two heats were held.

The swimmers with the eight fastest times advanced to the final.

9:54 9 September 2016:[1] 9:57 9 September 2016:[1] 18:11 9 September 2016:[2]