Merchistonian was a founding member of the Scottish Rugby Union and one of the five Scottish clubs to issue the challenge to English football players that resulted in the first rugby international,. The club supplied three players for the match Andrew Galbraith Colville, George Ritchie and the scorer of the match's only goal (conversion) William Cross. Cross also scored one of Scotland's two tries to England's one however, at the time, tries did not result in points merely a 'try' at scoring a goal and Scotland won the match 1-0.
In 2013, the Merchistonian Club (the School's FP society) launched an attempt to revive the FP rugby team under the name Merchistonian RFC. The side played its first match against traditional rival Edinburgh Academical FC with both sides fielding a strictly FP team (rather than Accies open first XV) at Raeburn Place on 29 March, losing 31-20. The intent is to play this fixture on an annual basis. Merchistonian RFC also competed in a number of sevens competitions and the Edinburgh 10s in 2014.