In the school seal are two circles. Inside the circles are the cross, the miter and the vacculo.
The cross is the symbol of Jesus. The vacculo is the symbol of the shepherd and the miter stands for high position held by Sto. Tomas de Villanueva, that of a bishop.
The seal should serve as a constant reminder to the students of their Christian vocation and to communicate the love of God through an active witness of charity, obedience and humility as what Sto. Tomas de Villanueva did therefore the school’s ideal graduate… “a living witness of God’s presence”.