Conception: The Diocese of Thuckalay, since its erection, has been pondering over the thought of extending its educational outreach in the field of higher education. Mar George Alencherry had set up a Diocesan Feasibility Study Team with priests, religious and lay leaders under the leadership of Rev. Fr. Philip Kodiyanthara, to explore ways to establish the kind of Institution for higher education by the Diocese in Kanyakumari District, which would cater to the needs of the poor and the downtrodden, irrespective of caste, colour, creed or gender, though ample opportunities needed to be provided to the youth belonging to the Syro Malabar Catholic Church in the District.

The Study Team, after series of consultations and deliberations arrived at a conclusion that the District had quite many engineering colleges and that the District, particularly, the Karinkal region needed College for Arts, Science and Commerce education. The Team suggested that the Diocese of Thuckalay establishes an Institution for Higher Education for Arts and Science education and that the existing regulations of the Manonmaniam Sundaranar University in Tirunelveli provided for commerce education to be included in an Arts and Science College and that the College be established in Karinkal region under Soosaipuram Forane of the Diocese.

The Diocesan Pastoral Council went through the report and appreciated the efforts of the Team and resolved to explore the idea of establishing an Institution for Arts and Science higher education. The Diocesan Council, apex decision making body of the Diocese, also decided to proceed with the recommendations of the Team and the Pastoral Council. The Council, however, set up a Committee under the leadership of Rev. Fr. Philip Kodiyanthara and Rev. Fr. Thomas Powathuparambil to find an appropriate location for the establishment of an Arts and Science College in Karinkal area. The Council also directed the Committee to look for land already available with the Diocese. The Committee explored all the locations where land was already available with the Diocese or Parishes and inspected them with the help of priests and lay leaders of the Diocese. In the meantime, Mar George Alencherry became the Major Archbishop of Syro Malabar Catholic Church, with its headquarter in Ernakulam, Kerala and Rev. Fr. Philip Kodiyanthara was made the administrator of the Diocese. The Committee suggested that the two plots of land, approximately 5 acres, almost opposite to the Soosaipuram Parish Church be the designated place for establishment of the Arts and Science College of the Diocese. However, there was a problem of a small plot of land exactly in the middle of the two plots of land, which needed to be purchased in order to connect the two plots. Rev. Fr. Philip Kodiyanthara, having known the local situation well, as he had been the Parish Priest of Soosaipuram, took up the task to arrange for the same. No further steps could be taken up as the Diocese was without a Bishop.

Establishment: After the consecration of Mar George Rajendran, SDB as the second bishop of the Diocese of Thuckalay, the new bishop did not let down the aspirations of the priests, religious and faithful of the Diocese and carried the dream forward and took the decision to establish the institute of higher education in Soosaipuram, Karinkal, and on the advice of the Diocesan Pastoral Council, named it as St Alphonsa College of Arts and Science. Rev. Fr. Anthony Jose, Parish Priest of Soosaipuram was appointed as the first Secretary and Correspondent of the College, which he continues to hold until now. Rev. Fr. Philip Kodiyanthara unfortunately passed away in February, 2013. Rev. Fr. Anthony Jose took up the efforts for buying the necessary plots of land in order to connect the two plots. All efforts were made by the Bishop, Rev. Fr. Thomas Powathuparambil and the Secretary and Correspondent for the speedy construction of temporary accommodation for the students of the College. On June 30, 2014, St Alphonsa College of Arts and Science was founded with 148 students in four departments of Commerce, English, Physics and Mathematics, in a glittering ceremony, which began with seeking of Divine Blessings through Holy Mass.

Present Status: Presently, St Alphonsa College of Arts and Science is a very pulsating, interwoven community where academic curiosity and creativity prosper. The present building was inaugurated on January 17, 2016 in an event attended by several dignitaries and participated enthusiastically by the students of the College. The Diocese desires to provide quality infrastructure, facilities and education to the poor, who otherwise will not be able to access quality education and facilities in a rural set up.

The College is affiliated to Manonmaniam Sundaranar University, Tirunelveli.  The College fosters to Higher Educational opportunities and job-oriented skill training facilities for poor and the marginalized.  The College offers special training, after the academic hours, from 3 PM to 4 PM in preparing the students for Bank Examinations, Entry in Government and Private Services, National Service Scheme, Sports and Games, Communicative English, Personality Development, and Basic Computer Education. The students join these courses and programmes according to their aptitude.

In the very next year of establishment, the College went on to introduce two more new courses, namely, BSc Chemistry and BSc Computer Science.

In 2017, the College went on to the next step and introduced Post Graduate Courses in MA English, MSc Mathematics and M.Com and in 2020 MSc Computer Science and MSc Physics have been introduced.