The present premises of the college has a history associated with various institutions functioning there earlier and it starts with Our Lady of Sorrows Church Pilathara. It was built by Italian Jesuit missionaries. It is Rev. Fr. Peter Caironi, the founder of Chirakkal Mission who bought the 10 acres of land at Pilathara in 1960. Rev. Fr. Linus Maria Zucol built the parish church in 1969, presently the college chapel. Along with the parish, Rev. Fr. Joseph Taffrel S.J built the two storied shopping complex, Navajyothi catechism centre and Nirmala Carpentry training centre at Pilathara. It is Rev. Fr. Joseph Chitooparambil who started Nirmala I.T.C. over here which was shifted to Embete, Pariyaram thereafter. There was a Nirmala parallel college also though it worked for a while only. It was in 1995, church construction started at the other side of the property and completed in 2002.

       St. Joseph’s College, Pilathara was established in 2005 and it was initiated by Bishop Varghese Chakkalakal, then Bishop of Kannur. The mission to establish a Self-Financing college was entrusted with Msgr. Clarence Paliath, then the Director of KAIROS, the official social service wing of the diocese. The diocese thought to have the college at Kotta Estate, near Puracherry, Pilathara. The University inspection team suggested to have the college at Pilathara town.

      The college started functioning at Navajyothi hall (old building) which was functioning as a retreat centre as well as animation centre for Chirakkal mission area. Before starting the college, the parish church was shifted to the other side of the property with presbytery, leaving whole area for college. College started functioning in 2005 with two courses B.Com and BSW. The first principal of the college was Dr. E.J. Thomas S.J, a veteran Jesuit priest retired from Loyola College Trivandrum. Fr. Clarence worked as Manager of the college as well as the Head of the Dept. of Social Work till 2012. Within a short period of two years Fr. Kaironi block of the college was completed to house the departments and classes in a better ambience. But Library, Principal’s Room, College Office etc. continued to work in the old building until Fr.Zucol block was built in the year 2013. Rev. Fr. Jacob Jose took charge as Manger In 2008, and Rev. Fr. Clarence assumed Principalship in 2012 making the college a notable place for its hospitality and upward mobility through his visionary interactions and management of everyday campus realities.

      In 2015 Rev. Fr. Johnson Simethy took charge as Manager and Assistant professor in the dept. of Social work. In 2016 Msgr. Clarence Paliath became Vicar General of the diocese and was transferred to Bishop’s House, Kannur and Dr. T.A John, then Vice Principal, became principal and Rev. Fr. Johnson Simethy was assigned the post of the Vice principal, with Rev. Fr. Joy Painadath as Manager. Dr. K.C. Muraleedharan, a well- known academician and former head of the dept. of English at Payyannur College, Payyannur became Principal in 2018. Rev. Fr. Shijo P.A, the assistant manager and Rev.Fr. Antony Pius the financial administrator of the college joined the college in 2019. In 2022 Rev. Fr. Benny Manappat joined as the financial administrator and Msgr. Dr.ClarencePaliath as Manager.

       Rev. Fr. Rajan Fausto appointed as the new manager in 2023.Dr. Denny Philip, Assistant Professor of Nirmalagiri College took charge as the new Principal in the same year. Dr. Subhash John, Head of the Malayalam Department appointed as the Vice-Principal. Rev. Fr. Melvin Devassy, appointed as the new assistant manager in 2024. The college is moving smoothly ahead to realize its mission and vision with the patronage of His Excellency Rev. Bishop Vadakkumthala, Bishop of Kannur Diocese in the last few years.