Groton is a school whose Episcopal chapel is host to many faiths. St. John's Chapel - a Henry Vaughan Gothic Revival masterpiece - stands at the main gates of the school, an invitation to explore the encounter between the human spirit and the divine. Four weekday mornings the school community begins its day in the chapel, encountering silence, music, prayer, readings from the sacred texts of many of the world's religions, and hearing the messages of students, faculty, alumnae/i or guests. Many find this start to each day to be one of their most important daily moments, experiencing comfort, challenge, peace, and refreshment.

Administered by twelve student Chapel Prefects and the Chaplains, the chapel program strives to be inviting and inclusive; students frequently offer prayers and readings from their own faith tradition or in celebration of the human spirit; speakers invite the community to see life through profound images, providing us an opportunity for personal growth in appreciation of, or reaction to a wide variety of opinions and experiences. In chapel, the mind may be challenged, the heart may be warmed, and the hands may be strengthened to serve.

On Wednesday morning, there is a celebration of the Holy Eucharist that students, faculty, and staff may attend on a voluntary basis. On Sunday, the required service is one of Morning Prayer, Holy Eucharist, or Evensong. Students eager to observe their own religious tradition may do so by arrangement with the Chaplain: Jewish students often choose to observe a Friday evening Sabbath service; Muslim students gather in prayer and study; Buddhist students find quiet time for meditation; and many Roman Catholic students attend Mass at the local parish.
Host to a number of concerts and seasonal services throughout the year, the chapel is also home to a set of tower bells that attract change-ringers from around the world, as well as the school's own student society of bell ringers.