Bejai was once a part of the Cathedral parish.  Because of the long distance from the church and the difficulties experienced by the people here, a land measuring 5.37 acres was obtained from the government in 1670 for a cemetery and a mortuary chapel was raised on the plot.  The priests from the Cathedral offered Sunday Mass here.

On March 22, 1912 Bishop Perini, sj gave Bejai a resident chaplain.  He was Fr Sebastian Noronha.  His successor Fr Joseph Peter Fernandes built a portion of the presbytery.  The present church was built in 1924 by Fr A.E. Colaco who had succeeded Fr Fernandes.  He also completed the presbytery and planned the belfry.  Fr Leo Saldanha completed it in 1937.  Fr Robert L.M. Pinto renovated the church. 

Fr Sebastian Noronha began the St. Francis Xavier  parish school.  Fr A.E. Colaco constructed the school building. Lourdes Central School was started by Fr Bernard D’Souza in 1999.  He constructed the new building for the school in 2000.  He put up the huge shopping complex and also the Hall as income generating assets to the church.