The men's 100m butterfly S13 event at the 2012 Summer Paralympics took place at the London Aquatics Centre on 31 August.

There were two heats; the swimmers with the seven fastest times advanced to the final, while because of tied times in the heats the eighth final place was decided by a swim-off.

PR = Paralympic Record.

AF = African Record.

Official London 2012 Paralympics Results: Heats Archived 2012-09-16 at the Wayback Machine Official London 2012 Paralympics Results: Final Archived 2012-09-16 at the Wayback Machine