When the seminary was erected in 2000, the synod of the church had a plan that visualized a steady growth of the seminary that would complete its full structure in eight years. As the seminary accordingly began in June 2001, there were 21 students from eight dioceses admitted to the course of philosophy, and four resident members on the staff: the first rector was Rev. Dr. Joseph Kuzhinjalil, D.C.L. (Diocese of Palai); Frs. Simon Valloppilly (Diocese of Thamarassery), Thomas Neendoor (Archdiocese of Tellicherry), and Jose Vettickal (Archdiocese of Tellicherry) were the other resident staff. Including the non resident professors, in the teaching staff there were then 12 members.

Since the newly erected seminary had no house of its own, it began its life in a nearby house belonging to Nazareth Sisters. The foundation stone for the new seminary building was laid on 3rd August 2002; subsequently, the completed philosophy block was blessed on 18th June 2003 by His Beatitude Mar Varkey Cardinal Vithayathil. The foundation stone for the theology block was blessed by His Beatitude Ignace Cardinal Moussa I Daoud, Prefect of the Congregation for the Oriental Churches Rome, on 10th January 2004, on the occasion of his visit to the seminary.

In the subsequent years after the inauguration, new batches of students were admitted, and more priests were added to the resident staff. At the same time some of the members in the staff returned to their dioceses. Frs. George Pulickal (Archdiocese of Tellicherry), Jose Pulavelil (Diocese of Palai), and Thomas Poovathanikunnel (Diocese of Kanjrappally) thus joined the resident staff in the academic year 2003-04. After completing a term as the rector and after finishing the construction work of the philosophy block, Very Rev. Fr. Kuzhinjalil, Finance Officer Fr. Vettickal, and Fr. Jose Pulavelil returned to their home dioceses.

Since May 31st 2004, Very Rev. Fr. George Pulickal had been serving as the acting rector and since 11th November 2004 he had been serving as the rector of the seminary.  In the same year Fr George Myladoor (Diocese of Mananthavady) was appointed as the finance officer of the seminary. Frs Paul Mudathotty (Missionary Society of St Thomas), Jose Muthanattu (diocese of Palai), and Thomas Kuzhuppil (Archdiocese of Changanassery) joined the resident staff in the academic year 2005-06; Frs. Jacob Chanikuzhy (Archeparchy of Ernakulam–Angamaly) and Thomas Padiyath (Archdiocese of Changanassery) joined the resident staff in the year 2006-07; Frs. George Mangalathil (Archdiocese of Changanassery) and Antony Tharekadavil (Archdiocese of Tellicherry) joined the resident staff in 2007-2008.

The construction of the beautiful chapel of the seminary was completed, and was consecrated on 26th July 2007. For the consecration ceremony, His Beatitude Mar Varkey Cardinal Vithayathil and several other bishops were present. On 29 January 2008, the first batch of the students, fourteen in all, received the holy order of M’samsanusa (diaconate) in the new chapel. The ordination ceremony was officiated by the convener of the ad hoc committee, His Grace Mar George Valiamattam together with His Grace Mar Joseph Powathil. On this occasion, twenty-three of the second batch also received their ordination as Heupadiyaknusa. In May 2008, Fr. Paul Mudathotty was elected as the Assistant General of the MST. He eventually left the seminary to enter upon the new office, while Fr Thomas Anikuzhikattil (Diocese of Idukki) joined the resident staff, who was subsequently appointed as the prefect of studies on 22 February 2009.

In the year 2008-2009, the first batch of 14 students got ordained priests for different eparchies, which was a landmark in the history of Good Shepherd Major Seminary. In the second batch, 22 students were ordained (2009-2010) and in the third batch 16 students (2010-2011). The list of these priest are available in the Alumni page.

In the beginning of the academic year 2009-2010 a new administrative body was appointed: Fr Joseph Muthanattu was appointed as the Finance Officer on 13 May 2009, Fr Thomas Anikuzhikattil as the Rector on 21 May 2009, and Fr George Mangalathil as the Prefect of Studies on 08 June 2009 in lieu of Frs George  Myladoor, George Pulickal, and Thomas Anikuzhikkattil respectively. After completing a term and another two years Fr George Pulickal left the seminary to take pastoral work in his own diocese, and Fr George Myladoor, after completing his term of office (Since 15t June 2004 till 15 May 2009), returned to his home diocese in May 2009. Fr Jose Koodapuzha from Diocese of Kanjirappally joined the resident staff in the academic year 2009-2010. In May 2010 Fr Sebastian Palakuzhy (Archdiocese of Tellicherry) was appointed Finance officer in lieu of Fr Jose Muthanattu, who was then relieved. Frs Joseph Mulanjanany (Diocese of Kothamangalam), Joseph Karukaparambil (Archdiocese of Kottayam)n and Mathew Pattamana (Archdiocese of Tellicherry) joined the resident staff in the beginning of the academic year 2010-2011.

Goal of the Seminary

The seminary wishes to train its students in such a way that they will become good pastors and ministers of the word of God. The Good Shepherd and Preacher Jesus Christ is the model after whom the candidate in the institute has to fashion himself (Ps 23:1; Jn 10:11). He should become a good and self-sacrificing leader of the Catholic Church. The people of God should feel safe under the protection of this shepherd of Jesus.

Giving personal attention to all the students is one of the main concerns of this institute.
The seminary therefore tries to create a home atmosphere in which all the students feel that their formation is safe under the guidance of the institute. Together with the intellectual training, they are given formation for spiritual and emotional growth: they are given three years of philosophy training which will be followed by an year of practical training and period of personal reflection (regency); then they will receive the clerical dress which will be followed by four years of biblical, theological, and pastoral studies.

Throughout the period of training, the students will get enough opportunities to form a personal prayer life, and to develop their personal talents.
The professors and the students together with their Good Shepherd are always in search of pastures which are the products of the ever changing periods of history. The candidates have to apply effectively their energies in order to form themselves for the church so that they can competently guide the people of God of the Catholic Chruch in India and abroad..