St. Joseph Academy was owned and operated by the Sisters of St. Joseph of Carondelet, whose motherhouse is in St. Louis, Missouri.  At the invitation of the Holy Ghost Fathers in charge of St. John the Evangelist Parish in Green Bay, six Sisters came to teach in the St. John School in August 1893, under the direction of Mother Herman Joseph O'Gorman.  In 1896, the Sisters began teaching advanced classes for young ladies.  They purchased the old Monastery of the Good Shepherd Sisters and, in 1898, there were 15 students at what was called the Academy.

By 1908, there were 31 students at the Academy.  The Sisters purchased the Kellogg buildings and property and as enrollment continued to grow they added on to the Kellogg House.  By 1910, the number of students had grown to the extent that it was necessary to erect a separate school building that connected to the Kellogg House.  This new high school opened in 1911, while the elementary school continued to operate in the Kellogg building.  In 1941 the elementary school closed due to the growth of the high school and the room it demanded.  Another major addition was completed in 1950.

There had been resident students at the Academy from 1903 until 1956.  However, transportation became more available, and it no longer seemed necessary for the girls to reside at the school.  The areas used by residents then became available for school use.  A Multi-Purpose Center (for all-school liturgies, assemblies and for use by the physical education department) was added in 1983.

St. Joseph Academy can best be summarized with the words of Sister Helen Zambrowicz, CSJ, principal from 1978 to 1984.  She said, "We have three main foci.  One, we stress the message of God.  The importance of the community is the second focus.  Third is the orientation to serve God and others."