In 1941, the Ministry of Public Works announced the construction of a new building in Alto de Sto António (neighborhood in Faro) to serve the lyceum education by then operating in the Jo?o de Deus Lyceum (the name Jo?o de Deus was given to the lyceum institution in honor of Jo?o de Deus Ramos), current facilities of Tom?s Cabreira Secondary School. The increasing number of students (school population of 700 students) and the consequent lack of classrooms for all subjects was the main reason for this decision. The construction works began two years later.
In 1948, the school is renamed to Faro Central Lyceum, for there is not another in the region. It is also this year that Faro Central Lyceum started working in the now completed building in Alto de Santo António. The opening ceremony was chaired by then Minister of Education Dr. Fernando Pires de Lima, took place on 1948, 28th April with the official handover of the building to the Ministry of Education.
18 years later, in 1966, was again renamed to it's previous name of Jo?o de Deus Lyceum.
After the revolution and change of government in April 25, 1974, the the Portuguese education system underwent major changes that were put into practice until 1979. The lyceum and techical education were eliminated in 1975 and superseded by the Unified General Courses and the 10th and 11th years (previously 6th and 7th years). Thus, in 1978, the Jo?o de Deus Lyceum became the Jo?o de Deus Secondary School (High School), with the 12th grade also covered starting the following year.
In 1986, the Portuguese education system again underwent major changes: the Unified General Courses (7th, 8th and 9th years) became the Basic Education 3th cycle therefore, thus resulting in the Secondary School no longer covering these school years and instead focusing only on secondary education (optional), which included the 10th, 11th and 12th years. This process wasn't immediate because, by then, the new schools (newly built or under construction) didn't have enough capacity for all students of the new 3rd Cycle of Basic Education, so the Jo?o de Deus Secondary School (High School) continued to teach the 9th year of education until 1990.
From 2009, Secondary Education became mandatory until the age of 18 years and / or its end.