Pakshikere was once a ward of Kinnigoly parish.  The parish priest of Kinnigoly parish, Fr Jacob Lobo got a plot donated by Mrs Elizabeth Miranda for a small chapel.   The foundation for the chapel was blessed on October 22, 1959 and the chapel was blessed by Bishop Raymond D’Mello on October 28, 1960, the feast day of St Jude Thaddaeus, famous for his healing and miraculous powers. 
On May 3, 1964 Pakshikere became a parish with Fr Stanely R. Pereira (1964-1973) as its first parish priest.  The existing church was built by Fr Stanely Pereira when he was the resident chaplain at Pakshikere.

On October 28, 2000, the grotto of Lourdes was inaugurated by the former Archbishop of Bangalore, the Most Rev. Alphonsus Mathias.   The plans are on to construct a new presbytery and shrine in the future.  Pakshikere is one of the pilgrimage shrines in the diocese of Mangalore.

Fr Stanely R. Pereira started St Jude’s Primary School.  Fr Basil Vaz has renovated the school building.