In 1862, the headmaster, John Ford, went to visit Matthew Arnold at Rugby, and saw the game of rugby football being played. He decided to introduce the game at Bootham, but failed to notice the shape of the ball. Thus on returning to York he introduced rugby with a round rather than an oval ball. Nor did he ever master the rules, so that the game was still in 1867 'an ill-regulated scramble for the leather by as many as could be got to take part!' As every school had its own set of rules, when they started to have matches against each other in the 1850s chaos ensued on the pitch, and in 1863 the Football Association was founded and rules were recorded trying to combine both the rugby version of football (where running with the ball, and tripping, charging and hacking were allowed) and the version used at Eton and other schools. These attempts failed as loyalty to the Rugby code was too strong and then the separate Rugby Union was founded in 1872.

Football matches played with Ackworth School (a sister Quaker establishment) began in 1881. Bedroom tournaments started three years later, and by the last decade of the century there were full fixtures for both cricket and football, a tradition that has been maintained down to the present day. Paper chases were frequently organised, with the whole school following the hares to the cry of 'Tally-ho' by the member of the pack who found the confetti. On one occasion on a farmer's property the owner claimed that the confetti was bad for his cows, to which the science teacher responded that he had tested the paper and found it didn't affect animals, and so the farmer let the school continue their pursuit on his land.

Bootham's most famous athlete was Philip Noel Baker who was a silver-medallist runner in the Olympic Games in Stockholm in 1912 (and was later awarded the Nobel Peace Prize in 1959 for his work on disarmament and internation peace). In more recent times, former scholar Sophie McGill has worked wonders for the fortunes of York City Football Club, just round the corner from the school!