Through the benevolence of Jerry Murphy '36, ground was broken in 1998 for the construction of St. Mary's Chapel. In providing for the chapel, he said, "My first overriding thought is gratitude - gratitude that I am in a position to advance the fortunes of Saint Ignatius High School and strengthen her ability to turn out a rounded Catholic man in the Jesuit tradition, preparing Men for Others." He noted that in his own class of 1936, five men became priests. He said, "It is my hope that under the roof of St. Mary's Chapel many young men will hear the call of God and answer 'Yes'."
According to Ron Payto, design architect for St. Mary's Chapel, the selected chapel design was based on the overall spiritual idea of the relationship between God, man and knowledge. He says, "The chapel will be a celebration, 'For the Greater Glory of God;' and will embody in architecture the mission of the school to prepare students who are open to growth, intellectually competent, loving, religious and committed to doing justice." He adds, "Throughout the design we incorporated forms and symbols that make clear and direct reference to the school's Jesuit spiritual ideal."