Catholic schools in Canada
The existence of Catholic schools in Canada can be retraced to the year 1620, when the first school was founded Catholic Recollet Order in Quebec. The first school in Alberta was also a Catholic one, at Lac Ste.-Anne in 1842. As a general rule, all schools in Canada were operated under the auspices of one Christian body or another until the 19th century.
In the early 19th century, there was a movement to take the responsibility for education away from individuals and make it more of a State function. Thus, governments allowed schools and school boards to collect taxes to fund schools. Previously, a combination of charitable contributions from the members of a particular religious body, supplemented with tuition fees paid by the parents of the students, had been the method of financing a school.
Nevertheless, an element of religious formation remained as this was considered a necessary part of educating the whole person.
As the Catholic minority played an integral part of founding and establishing the country of Canada, it was important to them that their rights to educate their children in Catholic schools be protected in the British North America Act (1867). In fact, when the Fathers of Confederation came from New Brunswick, Nova Scotia, Canada East, and Canada West to meet in Charlottetown and Quebec, they quickly concluded, in the words of one of the Fathers, Sir Charles Tupper, that “Without this guarantee for the rights of minorities being embodied in that new constitution, we should have been unable to obtain any Confederation whatever.” 
"The concept that church and state are partners, not hostile and incompatible forces that must be kept at a distance, has made it possible for educational authorities in Canada to subsidize Jewish schools in Québec and Hutterite schools on the Prairies, to condone Amish schools in Ontario, and to permit the Salvation Army to develop its own public schools in Newfoundland." 
The "public" school system was that of the majority of taxpayers in an area. In most of the English-speaking parts of Ontario, this tended to amount to a form of "common-core Protestantism." This was accelerated under the 1846 School Act spearheaded by Egerton Ryerson. He believed it was part of the Government's mandate to be a social agency forming children in a uniform, common, Protestant culture, regardless of their individual family backgrounds. Although working in Ontario, his ideas were influential all across Canada.
In Ontario, Alberta, and in other provinces, if there were enough families of a particular faith that wished to do so, they could set up a "separate" school, supported by the specially-directed taxes of those families who elected to support the separate school over the public schools. In practice, this gave a mechanism for Catholics to continue having their own schools. Separate schools tended to be Catholic in the south of Ontario whereas in northern Ontario, where the majority of people were Catholic, Protestants were the ones to set up separate schools. Yet, Catholic schools form the single largest system in Canada offering education with a religious component.
Starting in the 1960s, there was a strong push to remove all religious education from the public schools in Canada, although Catholic schools tended to maintain their religious character at least in theory if not always practice.
In the 1990s there was a further movement in many provinces to dis-allow any religious instruction in schools financed by taxes. Currently only seven of the thirteen provinces and territories still allow faith-based school boards to be supported with tax money (Alberta, Newfoundland, Ontario, Quebec, Saskatchewan, Northwest Territories, and Yukon (to grade 9 only)).
In 1999, the United Nations Human Rights Committee determined that Canada was in violation of article 26 of the International Covenant on Civil and Political Rights, because Ontario's Ministry of Education discriminates against non-Catholics by continuing to publicly fund separate Catholic schools, but not those of any other religious groups. For more information see Education in Canada and Waldman v. Canada.
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Schools in Quebec were organized along confessional lines until amendments to the Education Act took effect on July 1, 1998. Thus, just as in Ontario, there existed parallel Catholic and Protestant school boards, financed by taxpayers who chose which schools to support, but ultimately controlled by the Provincial Government.
Until the changes of 1998, the law in Quebec required all religion teachers in Catholic schools to actually be practicing Catholics. Religion courses at the time, while dealing with Theology and Church history, were more pastoral in nature, especially in elementary schools. It was thus assumed that a non-believer could not properly instruct children by modeling for them an adult living their Catholic Faith.
The changes of 1998 re-organized school boards along linguistic lines — English and French — and reduced their number, among other things. Catholic students no longer attend Mass. Teachers may lead children in prayer only when it is inclusive. Religion courses are still offered in schools, though students can choose to follow moral education classes instead. Furthermore, while schools in multicultural neighborhoods removed their crucifixes and requested name changes (most Catholic schools had been named after saints), those in Catholic or immigrant neighborhoods tended to passively resist the changes. For example, crucifixes still hang on classroom walls in many schools in the east end of Montreal, which is predominantly French and Italian.
Before the changes of 1998, each Catholic and Protestant school board had an English and a French sector. The importance of either sector varied from region to region and board to board.