The Carmelite Missionaries, who were sent to Malabar by Pope Alexander VII, started a small Seminary at Verapoly in 1682 for the formation of both the Latin and the Syrian clergy. Due to the lack of conveniences the Seminary at Verapoly was shifted to the new buildings at Puthenpally in 1866. In 1888, the Seminary at Puthenpally was constituted the Major Central Seminary for the whole of Malabar, and was placed under Congregation of Evangelization of Peoples. Owing to the increase in the number of students, a new Seminary with better accommodation was built at Mangalapuzha, Alwaye. The new Seminary was officially inaugurated on 28th January 1933. The increase in the priestly vocations necessitated further extension. On 24th November 1955 the new philosophical college at Carmelgiri was solemnly blessed and inaugurated by His Excellency Most Rev.Martin Lucas, then Apostolic Internuncio to India. In 1964 the Seminary was raised to the ‘Pontifical’ status by the Holy See. On June 12,1976, the direction and administration of the Pontifical Seminary was entrusted to the Kerala Catholic Bishops’ Council.
The first step towards the realization of the plan for a Faculty had been taken on October 7, 1959, when the Congregation issued a decree affiliating the theology department of the Seminary with the Lateran University, Rome. With this, the theology department of the Seminary became “Studium Theologicum” which was governed by norms given by the University and a convention between the Rector of the Lateran University and the Rector of the Seminary. In April 1971, the Kerala Catholic Bishops’ Council sent a petition to the Congregation for the erection of an autonomous Faculty. On February 24, 1972, the Congregation for Catholic Education issued the decree erecting the Theological Faculty in the Pontifical Seminary. The decree granted the new Faculty all the rights and privileges which were enjoyed by Theological Faculties. It also empowered the Faculty to confer suitable degrees to students who are successful in their studies and research. The power of conferring the degrees of Bachelor and Master (Licentiate) in theology was explicitly granted. On 15th February 1973, the Pontifical Institute of Theology and Philosophy, Alwaye, was officially inaugurated by His Excellency, the Most Rev.Dr.John Gordon, then Apostolic Pro-Nuncio to India. On 25th April 1997, through a decree the Congregation for Catholic Education separated the Pontifical Institute from the Pontifical Seminary. At present the Pontifical Institute functions at two separate campuses - Mangalapuzha and Carmelgiri, and offers simultaneously courses of theology and philosophy in both campuses.