The Natural History Society was started in 1834 by the Headmaster John Ford. It was called 'The Natural History, Literary and Polytechnic Society'. It had a lot of clubs that came under its aegis, concerned with Natural History, Archaeology, Astronomy, Botany, Conchology, Diaries, Entomology, Excursions, Geology, Astronomy, Botany, Meteorology, and Ornithology. Under the heading 'literary' there were essay societies, a lecture-, library-, and newspaper-club, senior class reading and discussion group; while under the heading 'polytechnic' there were art, gardens, and a photography workshop. Each year the Natural History Club put on an annual Christmas show with prizes.

In 1909 the Natural History Club had an exhibit at the Franco-British Exhibition. It was sent in response to a special invitation received from the British Education Section and it was conspicuous in consisting entirely of work done by boys in their out-of-school time. The 1909 edition of ‘Bootham’ notes that ‘The Natural History Society is now in its 76th year and with a record of close on 500 meetings, is the oldest society in the country of organising and furthering useful school hobbies.’

The society also made collections of fossils, birds eggs and historical files. In 1911 the membership of the club went up to 65 boys and several masters. The Natural History Club had many excursions. The outings to Castle Howard, Skipwith, Pilmoor, Kirkham Abbey and Scalby were perhaps the most successful in the year 1911. The Club celebrated 150 years in 1984, when the main address was given by the former pupil, Ted Happold.
Today, the society thrives in a different form, in the charge of the Biology department which has recently run expeditions including a diving trip in southern Europe and a visit to the Farne Islands and Iceland.