The Men's 100 metre butterfly S13 event at the 2016 Paralympic Games took place on 8 September 2016, at the Olympic Aquatics Stadium.

Three heats were held.

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

11:10 8 September 2016:[1] 11:13 8 September 2016:[1] 11:16 8 September 2016:[1] 19:32 8 September 2016:[2]