Pope John Senior High School and Minor Seminary has a vibrant chaplaincy headed by a chaplain who is appointed by the Archbishop of Accra. Among other things, the POJOSS chaplaincy is the headquarters for religious groups like the Catholic Students Union (CASU), Legion of Mary, Eastern Region and the Sacred Heart Confraternity in the Eastern Region.
It therefore sees to the organization of the St. Thomas Aquinas Day celebrations and Kwahu-Tafo pilgrimage held annually in the Eastern Region. The chaplaincy is currently headed by Rev. Fr. Joel Yao Kwame of the Roman Catholic Archdiocese of Accra.