Merchiston football is run through the Senior Sports Programme on Monday, Tuesday and Thursday afternoons. All boys who select the activity will attend training sessions to work on fitness, skills and game practice. The School has both a 1st XI and 2nd XI team that play fixtures against other independent schools and the 1st XI compete in the Scottish Independent Schools (SISFA) cup.
There is also opportunity for some to be selected for the SISFA squad to play against Scottish Universities and also England independent school (ISFA) select squad. Recently, three boys were selected and played many games for SISFA. Theo, a Gibraltar U21 international, played in the annual SISFA vs ISFA fixture in Manchester, with Scotland beating England for the first time away from home.