Stonyhurst College is Roman Catholic and has had a significant place in English Catholic history for many centuries (including more chequered moments such as the Popish Plot and Gunpowder Plot conspiracies). In 1803 the Society of Jesus was re-established in Britain at Stonyhurst and the school became the headquarters of the English Province. Until the 1920s Jesuit priests were trained on site in what is today the preparatory school. The school continues to place Catholicism and Jesuit philosophy at its core. The present chaplain is Father John Twist, SJ.
Stonyhurst is distinguished by the central and distinctive Jesuit ethos "creating men and women for others". The Jesuit mission statement is "Creating people of Good Judgement, Clarity of Thought, and Principled Leaders for the Next Generation".
The Jesuit ethos has three central components: Creating men and women for others Stonyhurst has a long and well-developed tradition of voluntary service, helping students to understand the problems faced by disadvantaged people. This tradition had evolved today into the Arrupe programme named after the Jesuit priest Pedro Arrupe from Spain. The programme places students in a wide variety of community settings with the aim that every student will have volunteered during their time at school. Students are encouraged to develop and use their skills to contribute to society; Medicine and the Law are popular career choices for example. One of the opportunities that students have through being part of the wider Jesuit community is the "Chiwirangwe" (a Shona word meaning 'we will struggle together') project that twins Stonyhurst with the Jesuit school, St Peter's Kubatana (in Zimbabwe). The project is organised as part of their Companions programme that twins all nine UK Jesuit schools with Jesuit schools around the world. Stonyhurst alumni have the opportunity to take a gap year working in Jesuit projects around the world.
Pupils run, under the supervision of adult trustees, their own charity, Learning to Care, raising money for various causes. St Mary's Hall has its equivalent called Children for Children. Each year the S.C.H.T. (Stonyhurst Children's Holiday Trust) Week takes place at St Mary's Hall. It is funded largely through the sale of Christmas cards and the Poetry Banquet, which is organised and managed by pupils. During the holiday week, as it is known, Poets and Rhetoricians (lower and upper sixth-formers) volunteer a week of their summer holiday in order to look after disadvantaged or disabled children from local schools, giving them an enjoyable holiday, with activities and trips out, which they would otherwise be unable to experience.