Shortly after the building of the stone church, it was decided that the thriving congregation of Holy Trinity should have a school. The old church building, which was on the site of the present rectory, was renovated and converted into two classrooms and living quarters for the Benedictine Sisters of Atchison, Kansas, who would staff the school.
In the fall of 1912, Sister Lucina and Sister Simplicia were the first Sisters to teach the children at Holy Trinity School, grades one through eight. The parish continued to increase in size and the school soon outgrew its building. In 1917, Fr. Haefele and the people of Holy Trinity decided to build a stone school.
Again, the parishioners donated part of the labor in order to save expenses and the stone was donated once again by the Zahners. Fr. Haefele worked side-by-side with his parishioners in the manual labor of this building project. The parish was blessed to have a number of mechanics, carpenters, electricians and stonemasons who were able to help with the building of the school. The school was built at a cost of $10,000. It contained three classrooms and living quarters for the Sisters.
For a few years, in addition to elementary grades one through eight, there was a four-year high school program. Because of shrinking enrollment in the high school, it was lowered to two years and then to a two-year business course. The business course had to be discontinued after a few years because most of the students stayed at home to help with the farm work after graduating from 8th grade. However, the elementary school enrollment increased steadily each year.