[5] Farmer returned to England to briefly work in his parents' millinery business, then travelled to Switzerland in 1853, marrying Mary Elizabeth Stahel (1840–1914) in 1859, the daughter of a Zurich schoolteacher, with whom he eventually had 7 children.

After teaching in Zurich for some years, John became music master and violin teacher at Harrow in 1862, reportedly appointed as a result of being noticed while giving piano demonstrations at the London International Exhibition.

[7][8] Affectionately known as "Sweaty John",[9] Farmer also introduced the smoking concert, or "Tobacco Parliament", that was held on Founder's Day, where school songs and musical contributions were welcomed from staff, boys and friends, with Farmer's items particularly memorable - he was remembered as a "capital entertainer" according to John Ivimey.

His proposed Sunday evening concerts in the College Hall were initially controversial when the performances on the Sabbath were strongly disapproved of by strict Sabbatarians.

He championed the music of Bach, editing two volumes for school students,[14] and his own oratorio "Christ and His Soldiers" was popular with smaller choirs.