It was founded as a German-style gymnasium (i.e., a combined high school and junior college) in Perry County, Missouri, in 1839.

In 1839, a group of Lutherans immigrated from Saxony, Germany in order to more freely practice their religion and settled in Perry County and in St. Louis, Missouri.

That summer, three candidates for the ministry who had not yet been assigned to a congregation, Johann F. Buenger, Ottomar Fuerbringer, and Theodor Brohm, began construction of a 1+1⁄2-story 16-by-21-foot (4.9 by 6.4 m) log cabin in the Dresden settlement just south of Altenburg.

The purpose of the school, as shown by the composition of the student body, was to provide a classical education to all children in the settlement.

[5] By May 1841, Buenger and Fuerbringer had left the settlement to serve as pastors elsewhere, and Brohm and Walther were unable to teach full time due to illness.

Under Loeber, the focus of the school changed to that of preparing pastors and teachers, with seminary training being added to the gymnasium curriculum.

In December 1849, the college and seminary, with nine students and one teacher, relocated to temporary quarters in that city, with the LCMS assuming ownership in October 1850.

A new two-story 42-by-43-foot (13 by 13 m) building housing both the preparatory school and the seminary opened on a 2-acre (0.81 ha) campus on South Jefferson Avenue in 1850.

On February 23, 1853, the Missouri General Assembly granted a charter to the combined institution under the name "Concordia College", the charter and legal name under which the now separate Concordia Seminary continues to operate [10] By 1860, the number of students in the preparatory school and seminary had increased, leading to overcrowding on the St. Louis campus.

Three professors, an assistant, and the 78 students {all male) of Concordia College moved to Fort Wayne in the summer of 1861, and classes began in September.

[11] However, inadequate housing due to the quickness of the move and a typhoid outbreak among both faculty and students made living conditions miserable.

The Seminary Building also housed the synod's teachers' college which had been relocated from Milwaukee, Wisconsin, in that same year,[13] but that school was soon moved off campus to relieve overcrowding.

The students and classrooms occupied the three-story central section of the structure, while the two-story east and west wings were used as faculty residences.

A house for the school's director and a duplex for two faculty were also built in that year, freeing up the space in the Seminary Building that they formerly occupied.

Excavation for what eventually was named Hanser Hall began in 1863, but work was halted due to the Civil War and lack of funding.

On July 12, 1866, synod president C. F. W. Walther indicated his support for the college's director, G. Alexander Saxer, who had held the position since 1858 and took a stern approach toward discipline.

Enrollment increased to about 300 students, but his requests to the synod for assistance were not heeded, leading Hanser to becoming physically exhausted and ultimately resigning in 1879.

The college's main objective was to provide the students with organized physical education along with the discipline that a military program instilled.

[28] In 1920, the leaders of the Fort Wayne Luther Institute, a two-year business and secretarial school founded in 1916,[29] proposed a merger with the college's high school department, and the faculty asked the synod to add courses not related to seminary training, but no merger occurred.

[31] Classes were originally held on the second and third floors of Hanser Hall after renovations paid for by the Lutheran churches in Fort Wayne.

[32] Concordia College stopped admitting high school freshmen into its ministerial program in September 1951.

[39] In addition to the approximately $1 million from the sale, $400,000 that had been earmarked for improvements at the old campus were directed to the senior college construction.

As was typical of the German model of education, instructors were given little flexibility in teaching techniques and students were expected to obediently master the material.

[48] The language issue became even more complicated in 1921, when the Slovak Evangelical Lutheran Church began sending its pre-seminary students to Concordia, necessitating the addition of Slovak-language classes.

[49] Notices began appearing in the college catalogs in the 1920s that emphasized the expectation for students to become fluent in German and Latin.

Opponents consisted of local and nearby independent teams until the school joined the Indiana Intercollegiate Conference sometime after that body's establishment in 1922.

Several Concordia team members, including Max Carey and Bill Wambsganss, later played in Major League baseball.

However, the sport was revived from 1926 until 1932, when it was again dropped due to the expense, injuries, and lack of other junior college competition.