Saints Mary and Joseph Church, Valparaiso, Nebraska had its beginning in two parishes. One was the St. Joseph Church in Agnew, which was founded in 1888 with Fr. William Murphy as the pastor. St. Mary's Church in Valparaiso was founded in 1913 with Fr. Alois Faessler as the first pastor. Shortly after the founding of St. Mary's, due to a shortage of priests, Agnew was made a mission parish to the new Church in Valparaiso.

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In 1975 the two parishes were merged into one parish, with Fr. John Glaves as pastor. The new parish became known as Saints Mary and Joseph Church. A new church was planned and built, big enough for all the people of both parishes. The new church was dedicated August 21, 1977.