1922: A convent was built by Franciscan Missionaries of St. Joseph (FMSJ) in Jesselton now known as Kota Kinabalu on a piece of land in Jalan Tunku Abdul Rahman which is later named Jalan Selatan. Sister Rose Charnley and Sister Gerarda Bonengaar who was from Inabong and Limbahau was placed in Jesselton to build up St. Father Valentine Weber and Mr. Tay Bee Chuan, St. Francis Convent was the first
successfully built all-girls school in Sabah. This school was divided into two portions, one to teach pupils English and another is to teach pupils Chinese.
1938: School's ground was enlarged due to the increase of students.
1942 - 1945: Due to the blaze of World War Two, all school's activity was halted. On January 1943, all nuns and priests were sent to Kuching, Sarawak until Japan surrendered in August 1945. The war destroyed St. Francis Convent and all its records.
1946 - 1952: The school was rebuilt and all activities resumed as before. Preschool classes even began with 15 pupils. Francis was equipped with a boarding school to accommodate the increase in students. Uniforms were later introduced and changed a few times and finally replaced with uniforms used until 1972.
1955: A block was separated in Jalan Tunku Abdul Rahman on the same land, beside a building. This block was later used as primary school from 1965 to 1993.
1959: A new building was built in Jalan Kebajikan which was later known as Jalan Harrington which is now the school's site. The school's construction idea was from Mother St. John. All donations that were needed for the project were sincerely donated by parents, students, ex-students, friends and the Ministry of Education. This new building was designed by Mr. Morley, an architect from Boory & Edwards. While the contractor for this building was from the Metropolitan Construction Company.
1961 - 1969: In 1961, a new building was officiated by the director of Education Department, Mr. G.D. Muir. Prefect systems were introduced in school later in 1962. St. Francis Convent preschool was moved to a new site in Jalan Kebajikan opposite of St. Francis Convent Secondary School. When Sabah joined the West in forming Malaysia, this school was placed under the Ministry of Education under the Education Law in 1961.
1969 - 1978: After being administrated by the nuns from the west (White Franciscan Sisters) for more than 50 years, finally St. Francis Convent was handed over to local nuns (Franciscan Sisters). Sister Mary Cecilia was elected as the headmistress for the secondary school in January 1971. The administration board was formed in 1972. In 1977, bridge classes were first held.
1979 - 1993: Due to the increase in students, classes during the afternoon were suggested and started in 1979. The school's Parents And Teachers Association Board (PTA) was formed in 1971, which consisted of parents and teachers. Francis Convent Primary School was successfully moved to Bukit Padang, Kota Kinabalu and the school's board planned to move the secondary school to the same site. The Primary School was moved because of a termite infestation. It was the contributions and cooperation of the school, PTA (Parents And Teachers Association Board), the body of administration and financial help from the government that has ensured the survival of St. Francis Primary School.
1999 - 2002: The constructing building of the new school's board was formed and the constructing building was launched at the year 2002.
2012 : A total of 46 students from Form 1 and 2 SMK St. Francis Convent was rushed to Queen Elizabeth Hospital 1 (QEH 1), here after the attack was believed to have hit the itch pollen poisonous plants as the rally at the school, yesterday afternoon. Incident took place at 3 pm when they attend a rally before one by one to complain itching on the hands, neck and face suddenly. Consequently, most teachers have to bring the students to the hospital an hour later. Of them, 32 were brought for treatment at the QEH 1, while 14 more to QEH 2 in Luyang.
