Catholic orders ran the school for most of its history. The school was run first by the Diocese of Victoria between the years 1890-1907. In 1891, the Sisters of St. Ann accepted a request to assume the matronship of the school, and remained in that position until circa 1973 . In 1906 operation of the school was taken over by the Missionaries of the Company of Mary (Montfort Missionaries), and they ran the school until 1957 . At this point the Oblates of Mary Immaculate (OMI) took over and ran the school until 1969. From April 1, 1969 until its closure in June 1975, the school was administered by the government.

When the school officially opened in July 1890, there were 16 boys in attendance. In 1891 12 females registered and the school continued to be co-educational. The school reached a maximum capacity of 115 children in 1961. Children who went to the residential school were isolated from their community, and frequently forcibly taken from their families. They were forbidden from speaking their language at the school, suffered neglect, were underfed, and often faced sexual, physical and mental abuse.

Children who went to the residential school were isolated from their community, and frequently forcibly taken from their families. They were forbidden from speaking their language at the school, suffered neglect, were underfed, and often faced sexual, physical and mental abuse.

In 1906, the water supply of the school became tainted, causing children to get sick. And in 1908, when the school was less than twenty years old, the principal was already petitioning for a new building. He described the current building as “insanitary” [sic] and “ruinous.” There was “insufficient air capacity and want of ventilation in some rooms, state of decay on the ground floor and foundations in the boy’s [sic] building, irregular and insufficient heating.” Even when a new school was opened in 1916, the principal noted that “from a sanitary point of view our [new] buildings are far from perfect…” Even as recently as 1968, a mother of a student at the school wrote two letters complaining about conditions, noting the pungent odor of bed-wetting and that her child's face and feet had sores that had not yet received any attention. It is noted in this same correspondence that the mothers of other children complained of nits. Food shortages at the school were also recorded, and one Principal even noted that complaints about food hurt recruitment. The punishment of children was often cited due to stealing food.

Between the years 1903 and 1920 the administrators of the Kuper Island school undertook eight separate surveys that outlined the status of former pupils. The survey for 1915, the 25th anniversary of the school opening, showed that of 264 former students who could be accounted for 107 were dead. Throughout the school’s years of operation, there are recorded occurrences of students suffering from mumps, measles, whooping cough, smallpox, chicken pox, paratyphoid B infection, tuberculosis, typhoid fever, skin disease, lice, impetigo, jaundice and dysentery (shigellosis). A smallpox epidemic struck the school in 1920, and there was a typhoid outbreak in 1939. Tuberculosis is particular highlighted in the archival record, and in 1947-48, 13 of the 100 students attending the school were hospitalized with tuberculosis. During the history of school, several children drowned trying to escape by swimming across to Vancouver Island, making use of small boats, or floating logs across the water. In June 1966, a boy hanged himself in the gymnasium of the school

Student complaints about food hurt recruitment. Students set fire to the school in Nov 1895 when holidays were cancelled. The numerous runaways, especially considering that the school was on an island, demonstrates resistance. Indian agent R. H. Moore wrote in 1946 that he thought there were “entirely too many runaways from this School”. Instances of parental resistance to children being taken to the school have been recorded. Parent also attempted to, and sometimes did, remove their children from the school.

The Kuper Island school had a conduct book in which student misbehaviors and punishments were recorded. The entries for the late nineteenth century and early twentieth century list numerous examples of students being punished for taking food. Punishments here included having to kneel during supper hour, confinement, whipping/lashing/strapping, hitting to the head, ear pulling, and being put on bread and water diets. A former staff member at the school describes witnessing one of the nuns at the school beating five or six students at one time in “a total rage.” The same person also witnessed students having their mouths washed out with soap for speaking an Aboriginal language. Several instances of lateral violence between students are also cited in the archival record. There were also several cases of sexual abuse. In January 1939, six boys escaped by canoe from the school. Upon being apprehended by the British Columbia Provincial Police, two of the boys were questioned. This questioning led to allegations of sexual and physical abuse by staff and clergy at school, which itself led to a full investigation of abuse at the school. The investigation involved the police on one side, and the school, church and Department of Indian Affairs (DIA) on the other. From Indian Affairs point of view, the reputations of the school and the church were viewed as being more important than the investigation and prosecution of any wrongdoer. The BC provincial government was giving active consideration to the prosecution of the main suspects, but when the school and Indian Affairs colluded in advising the suspects to leave the province, the investigation stalled and eventually shut down. Glenn Doughty, who joined the Oblates in 1960, worked at the school as the child-care worker for the senior boys until December 1972. He was arrested in 1990 and charged with five counts of indecent assault and five counts of gross indecency, for abuse he had committed at Williams Lake Residential School, which he was employed at prior to Kuper Island. He was sentenced to one year in jail. Four years later, he pleaded guilty to charges of indecent assault and gross indecency arising from his abuse of students at the Kuper Island school. He was sentenced to another four months in jail. In 2000, thirty-six more charges were laid against him for the abuse of students at both the Williams Lake and Kuper Island schools. He was sentenced to an additional three years in jail. In a 2022 CBC Podcast on the Kuper Island Residential School, accusations of sexual and physical abuse by former Kuper Island Residential School employee Brother Brian Dufour were also brought forth through Survivor testimony. Although not formally charged for offences at the school, Dufour was later arrested on abuse charges in April 2000, pertaining to his time of employment at a youth facility in Cornwall, Ontario – he died before full prosecution could be undertaken.

The Penelakut Band had the buildings of the former Kuper Island Student Residence demolished in October 1985.

Examples of Kuper Island Residential School survivor testimony can be found in the report "The Survivors Speak: a report of the Truth and Reconciliation Commission of Canada" (2015), in a CBC Podcast series on the school, and at Legacy of Hope Foundation ; and information sources about residential school history in British Columbia are being collated by the Indian Residential School History and Dialogue Centre at the University of British Columbia.