In Canada these are usually Roman Catholic schools which are run parallel to the public school system which historically had been either Protestant or Roman Catholic, but which in recent years has become secular. The separate schools in Ontario, however, are fully denominational and not secular. In addition to Roman Catholic school boards, Alberta and Ontario each have one Protestant separate school district.
Protection of the Separate School system was a major issue of contention in the negotiations that led to Canadian confederation, due in large part to racial and religious tension between the (largely Francophone) Roman Catholic population in Canada and the Protestant majority. The issue was a subject of debate at the 1864 Quebec Conference and was finally resolved at the London Conference of 1866 with a guarantee to protect the separate school system in Quebec and Ontario.
In the Quebec education system there were separate Protestant and Catholic school systems until 1998 when the system was replaced with linguistically based secular school systems. Similarly, Newfoundland and Labrador had schools organised on a confessional basis with separate denominational schools for Catholics, Seventh-day Adventists, Salvationists, Pentecostals, and an integrated stream. This was abolished by referendum in 1997 and a single secular system was introduced to replace the previous streams.
The question of separate schools has been most controversial in Ontario and Manitoba. The ending of public support for separate schools in the latter province in the 1890s prompted a national crisis known as the Manitoba Schools Question, and led to Pope Leo XIII's papal encyclical Affari Vos.
In Ontario, funding for the Catholic separate school system was initially only guaranteed until grade nine under the British North America (BNA) Act. This funding was gradually extended until 1984 when the government of William Davis extended funding to include the last three (Grades 11-OAC) years of secondary school after having rejected that proposal fifteen years earlier. The historically Protestant system was eventually transformed into the present day public board, and school prayer was banned in the early 1980s.
A province-wide newspaper survey conducted between 1997 and 1999 in 45 dailies indicated that 79% of 7551 respondents in Ontario favoured a single public school system. But rumours that the Catholic Church had instructed its parishioners not to respond to the survey suggest that it may have produced inaccurate results. Regardless of whether the results were accurate or not, no widely supported movement to amend the Constitution Act, 1867 has developed.
In Ontario the only separate schools are Catholic (except for one elementary school in Penetanguishene, Ontario, the Burkevale Protestant Separate School, under the Penetanguishene Protestant Separate School Board, which has no other schools); other faith groups do not receive similar funding. This restriction has often been criticized as contrary to the spirit of official multiculturalism: for instance, a Catholic teacher can be employed by either the public board or by the separate Catholic board, while a non-Catholic can only work in the secular system. The provincial policy has been ruled as discriminatory by the Supreme Court of Canada, and on November 5, 1999 the United Nations Human Rights Committee condemned Canada and Ontario for having violating the equality provisions (Article 26) of the International Covenant on Civil and Political Rights. The Committee restated its concerns on November 2, 2005, when it published its Concluding Observations regarding Canada's fifth periodic report under the Covenant. The Committee observed that Canada had failed to "adopt steps in order to eliminate discrimination on the basis of religion in the funding of schools in Ontario."
In Alberta in some areas that were originally populated by Franco-Albertan French Catholics before the province came into existence, the Catholic church controls the public schools and the separate schools are Protestant. This applies to St. Albert. Ontario also has a Protestant school board in historically French Catholic Penetanguishene. The Penetanguishene Protestant Separate School Board operates one elementary school, Burkevale Protestant Separate School.