For many years, there was no Catholic Church in Linden. Catholic families in the area traveled to Stockton to attend mass at St. Mary's Church on Washington Street or to St. Joachim's in Lockeford which was the church for Lockeford, Clements and Lodi. Holy Cross Church was designated as a mission of St. Joachim's in 1882 by Arch-Bishop Alemany of San Francisco. From 1882 to 1904 all records of important events such as baptism, frist communion, confirmation, marriage and death were recorded at St. Joachim.
In 1904, St. Anne's succeeded St. Joachim as the parish church for the area with Holy Cross becoming a mission of St. Mary's in Stockton, where records for this period can be found. Placed under the jurisdiction of St. Gertrude's in 1913 until 1921. In 1915, a church was built on the present parish property. Then placed as a mission church of St. Michael's, which had also remained a mission church until that date.
The community out grew the old church, and that wood frame building was moved to the rear of the property to make way for a new church.The present stucco church was built in 1953, and was dedicated on April 4, 1954. It was constructed by Stockton builders, Ben Merlo and Dan Nomellini.
The beautiful cathedreal style stained glass windows were created by Carl Huneke, Century Stained Glass Studio, San Francisco. The windows were installed in 1954 shortly after the completion of the church. Families of the parish community donated the windows.
In 1962, the Diocese of Stockton was established and Holy Cross Catholic Church became a parish with Msgr. Walter Doyle serving the community from 1962 to 1966.
The rectory, designed by architect Edward C. Merlo was added in 1975. The activities and classrom were completed in 1996.