Following the Civil War, universal public schooling, separate by race and unequal, began at the primary level in the South. In the North, government regulatory activity increased. Private schools, especially those religiously affiliated, were often looked upon as being "un-American." This allegation was hurled at Roman Catholic schools, in particular, founded as a defense against first the pan-Protestant nature of public schools, and second the secular, "Americanizing" school, each of which was perceived as a threat to the faith of a poor, besieged, immigrant population. Despite the widespread poverty of its members, the Catholic Church continued to found and operate parish elementary schools, able to do so because of the dedication of a teaching corps of vowed religious women, commitment from its members, the drive of its leaders, and ethnic concerns. The sometimes violent activities of the Know-Nothing Party, the American Protective Association, and the Masons that were directed against Catholics testified to the depth and breadth of anti-Catholic prejudice in American society, prejudice that was fanned by some statements of Catholic leaders, for example, the Syllabus of Errors by Pope Pius IX in 1864. Other denominations had also established private elementary schools. The Old School Presbyterians, for example, established almost 300 schools in the mid-nineteenth century, mainly because of concern over the alleged secularism of the common schools. For the most part, with the exception of the Lutheran Church-Missouri Synod, the schools founded by Protestant denominations did not endure.

Statistics for the percentage of enrollment in American K–12 private schools in the latter part of the nineteenth century reveal that in 1879 private secondary enrollment made up 73.3 percent of the total; by 1889–1890, in the wake of the growth of public secondary education, that figure had dropped to 31.9 percent. By 1900, 7.6 percent of the total school enrollment was in private schools.

In the latter years of the nineteenth century, government regulatory activity in educational affairs increased. Doubts were cast on the ability and desire of some private schools, especially those with an "old-world" connection, to foster citizenship among their pupils. Laws were passed, as in Wisconsin and Illinois, that attempted to control or perhaps eliminate private schools. In 1889, for instance, Wisconsin passed the Bennett Law, which defined a school as a place where the subjects were taught in the English language and which required students to attend a school in the public school district within which they resided. Following a bitter political campaign, the law was repealed, in large measure because of the efforts of a Catholic-Lutheran alliance, many of whose schools were threatened because of their adherence to the German language and customs.