The University of Edinburgh was founded by Royal Charter in 1583, and is the fourth oldest university in Scotland, after St Andrews, Glasgow and Aberdeen. The Old College on South Bridge opened in the 1820s. As the institution continued to expand, new buildings were constructed around George Square, where the heart of the university remains, and the King's Buildings campus in southern Edinburgh. A third campus at Little France was established in 2002. Development of the University's estate continues on all three campuses in the 21st century.

The Royal College of Surgeons of Edinburgh and the Royal College of Physicians of Edinburgh were established by Royal Charter, in 1506 and 1681 respectively. The Trustees Drawing Academy of Edinburgh was established in 1760, an institution that became the Edinburgh College of Art in 1907.

In the 1960s Heriot-Watt University and Napier Technical College were established. Heriot-Watt traces its origins to 1821, when a school for technical education of the working classes was opened. Heriot-Watt continues to have a strong reputation in engineering, and is based at Riccarton, in the west of the city.

Napier College, renamed Napier Polytechnic in 1986, gained university status in 1992. Napier University has several campuses in the south and west of the city, including the former Craiglockhart Hydropathic (of Siegfried Sassoon and Wilfred Owen fame) and Merchiston Tower (the family home of John Napier). The University contains several specialised research centres (including the Centre for Timber Engineering, the International Teledemocracy Centre and a large business school. In 2005 the University secured Skillset Screen Academy status for its film courses and now operates (in conjunction with Edinburgh College of Art) the Screen Academy Scotland, one of six accredited centres in the UK.

Queen Margaret University was founded in 1875 as a women's college, and today specialises in healthcare, theatre, media, hospitality and business.

Other colleges offering further education in Edinburgh include Telford College, opened in 1968, and Stevenson College, opened in 1970. Basil Paterson offers courses in languages and teaching. The Scottish Agricultural College also has a campus in south Edinburgh.

Edinburgh schools include Donaldson's College and the Royal Blind School, Scotland’s national residential and day schools for deaf and blind students, both of which serve Scotland and the north east of England. The Royal High School is considered to be the oldest school in Scotland.

Edinburgh also has several independent schools including: Stewart's Melville College, The Mary Erskine School George Heriot's School, Merchiston Castle School, George Watson's College, St George's School For Girls Loretto School, Edinburgh Academy, and Fettes College.