The history of the parish can be traced back to the 1840s when a number of German American families came to the area from Ohio in search of farmland.
St. Boniface Parish began with the first Mass offered in the village of New Vienna by Bishop Mathias Loras on January 6, 1846.
In 1848, the first permanent structure was built. This wood building measured 24 feet (7.3 m) by 30 feet (9.1 m) and had walls that were 10 feet (3.0 m) high.
By 1853, the population had increased to the point that a new structure was needed. Construction of this new church was completed in 1855. The church was 64 by 100 feet (30 m) with 22-foot (6.7 m)-high walls. A local resident, William Steffen Sr., was sent with two teams of horses to get three bells for the church. He arrived back in New Vienna just before Easter; the bells were raised in time to chime for the first time on Easter Sunday. This second structure was used until 1887.
In 1882, Father Frederick Pape returned to the parish of his youth and directed the building of the present Gothic church dedicated by Bishop Hennessy in 1887.
In 1887, the third and present building was completed. This building is 172 feet (52 m) long by 62 feet (19 m) wide. The walls are 35 feet (11 m) high. The stained glass windows are 14 feet (4.3 m) wide by 30 feet (9.1 m) high. The steeple is 200 feet (61 m) high.
The church has five altars made of carved wood which are still present in the church today. The old high altar was built by E. Hackner of La Crosse, Wisconsin.
The organ was built in 1891 by the Schuelke Organ Company. The organ at St. Boniface is one of the few intact Schuelke organs that still exist today. Aside from regular maintenance, the organ has remained basically unaltered over the years. One of the few alterations made to the organ was the addition of an electric blower in the 20th century.
From the parish there have been 34 priests ordained to the priesthood and more than 50 women religious.