Bishop Alexander McGavik announced the establishment of Blessed Sacrament Parish in June, 1937. Its first pastor was Monsignor Victor Plecity who was overseer of the building of a church-school combination building. The first floor of this building served as a temporary church, while the classrooms were occupied by 261 students. The first graduating class of Blessed Sacrament School was comprised of 30 students in June, 1939. The school was originally staffed by eight Franciscan Sisters of Perpetual Adoration from St. Rose Convent for grades 1-8. The Franciscan Sisters of Perpetual Adoration served Blessed Sacrament School until May, 1990.

An addition was built to Blessed Sacrament school in 1955 making the total number of classrooms 13. In 1967, the second addition to the school building brought new offices, a faculty room, three more classrooms, a library, and a gymnasium/auditorium. The last major remodeling of the building occurred in 1995 when a Library/Media Center, General Music, and Phy. Ed. office was constructed.

A half-day kindergarten program was added to the offerings at Blessed Sacrament School in 1985. In August 1992, the Catholic parishes of La Crosse, under the direction of Bishop John Paul joined together to open Aquinas Middle School to serve seventh and eighth grade students from the greater La Crosse area. Blessed Sacrament School would now house students in grades kindergarten through six. A full day, everyday kindergarten program was started at the school in 1993. In 2003, Blessed Sacrament School added a four year old kindergarten program to its offerings. 

January 1999 brought the announcement from Bishop Raymond Burke of the formation of Aquinas Catholic Schools to begin in August of 2000. Fourteen cooperating Catholic parishes of the area would work together to support and govern Aquinas Catholic Schools. St. Thomas More Parish School was closed with this announcement. In June of 2002, Holy Trinity School closed. After much consultation, February 2005 brought the announcement of a major change in the configuration of Aquinas Catholic Schools by Diocesan Administrator, Msgr. Richard Gilles. In the city of La Crosse, families choosing Aquinas Catholic Schools would for the 2005-06 school year enroll students, 4K through grade 2, at Cathedral School and students in grades 3-6 at Blessed Sacrament School. The decision included the closing of Mary, Mother of the Church School and St. James School. These difficult decisions have brought financial stability to Aquinas Catholic Schools. The fourteen Catholic parishes supporting Aquinas Catholic Schools and Bishop Jerome Listecki (installed in March 2005) believe in the mission of Catholic education and are poised to continue to insure the availability of Catholic education for the generations to come.