In the Middle Ages there was education in Kirkjubøur offered by the Catholic Church. According to the Sverris saga, Sverre of Norway received schooling by Roe the bishop of Faroe Islands; later speeches of his, show that he was taught Latin, a feature revealed by his knowledge of the Decretum Gratiani. The school in Kirkjubøur continued until the Protestant Reformation. After the reformation Latin Schools were established in the Danish kingdom, extending over today's Denmark, Iceland, Greenland, Faroe Islands, Skåneland and Gotland in Sweden, and Øsel (now Saaremaa) in Estonia. The Latin School in the Faroe Islands is first mentioned in 1547, in a letter to Thomas Koppen who got the Faroe Islands as a fief.

In 1870 the Faroese Teachers School (Faroese: Føroya Læraraskúli) was established to offer training and qualification for teachers. The first maritime schools were founded as private institutions in Tórshavn in 1893. The first Evening School was founded in 1904, with joint financing by the Løgting and Denmark. In 1912 a Danish Royal decree established compulsory primary education, with the provision that teaching was in Danish. That decision led to tensions in education as Faroese teachers Louis Zachariasen and Jákup Dahl continued teaching in Faroese and were persecuted for doing so; the issue was resolved in 1938 when Faroese was recognized as equal to Danish in Faroese schools. In 1927 the Danish government, upon the request of the Faroese parliament, established a public navigational school in Tórshavn, followed by a marine engineers school in 1929.

The Faroese Nursing School was established in 1960 by the Ministry of Health and Social Affairs; it traces its roots back in 1910 when nurses were trained in the hospital of Tórshavn. The University of the Faroe Islands, was established in 1965; Klaus H. Jacobsen, a Dane, was appointed as the first lecturer in 1970 to teach courses for the examen philosophicum, a prerequisite at the time to pursue higher education in Denmark. After Denmark abandoned the examen philosophicum in 1971, on the initiative of Jacobsen and Kjartan Hoydal the university accepted its first full-time science students in the autumn of 1972. Education in the Faroe Islands was administered by Denmark under the Home Rule Act, until in the late 1990s its administration was transferred to the Faroese government as a matter of local interest.

In 1979 responsibility on educational matters started transferring from Denmark to the Faroese authorities, with the Faroese government getting full economic responsibility of education in 1988. By 1996 education became the responsibility of the Faroese government; this procedure was completed in 2002, preceded by the establishment of the Ministry of Education, Research and Culture. The administration of the Nursing School was passed to the Ministry of Education, Research and Culture in 2000 and the degree was recognized as a bachelor's degree in 2003. In 2005 the marine schools of navigation and engineering merged to form the Centre of Maritime Studies and Engineering. On 1 August 2008 the Faroese School of Education and the Faroese School of Nursing where incorporated into the University becoming its departments.