The roots of Higher Education in Thrace date back to the foundation day (1488) of the Medical School in the complex of Sultan Bayezid II. Basic medical sciences of the period were taught in this school where 18 students received theoretical and practical education of medicine each year. Its hospital was the practice place of the educational institution. The foundations of function of the educational and application hospitals of nowadays were laid in these institutions.

In the Republic Period, Trakya University was established on July 20, 1982. There were three institutes (Social Sciences, Natural Sciences, Health Sciences), four faculties (Faculty of Medicine, Engineering-Architecture, Science and Letters, Tekirdağ Agriculture), two colleges (Edirne Education, Çanakkale Education), four vocational high schools (Edirne, Çanakkale, Kırklareli, Tekirdağ).

Later, four faculties (Faculties of Engineering, Çorlu; Economics and Administrative Sciences; Education, Edirne; Technical Education, Kırklareli;); two colleges (State Conservatory, Kırkpınar Physical Education and Sports College); sixteen vocational colleges (Edirne, Kırklareli ve Tekirdağ Vocational Colleges of Health Services; Vocational Colleges of Hayrabolu, Keşan, İpsala, Malkara, Lüleburgaz, Şarköy, Uzunköprü, Babaeski, Çerkezköy, Marmara Ereğlisi, Havsa, Muratlı, Saray) were established.

Afterwards, one institute (Balkan Research), six faculties (Faculties of Fine Arts, Health Sciences, Science, Letters, Pharmacy and Dentistry), three colleges (Foreign Languages, Edirne and Keşan Applied Sciences Colleges), six vocational schools (Edirne Social Sciences, Edirne, Technical Sciences, Kırklareli Social Sciences, Kırklareli Technical Sciences, Arda, Tunca), Research and Application Centers were added to Trakya University.

Among the academic units of Trakya University, during the rectorate of Enver Duran, those in Çanakkale transferred to Çanakkale Onsekiz Mart University in 1992, those in Tekirdağ transferred to Namık Kemal University in 2006, and those in Kırklareli transferred to Kırklareli University in 2007.

Now that, there exists ten faculties (Medicine, Engineering and Architecture, Economics and Administrative Sciences, Education, Fine Arts, Health Sciences, Science, Letters, Pharmacy, Dentistry), four institutes (Social Sciences, Natural Sciences, Health Sciences, Balkan Research), five colleges (State Conservatory, Kırkpınar Physical Education and Sports, Foreign Languages, Edirne Applied Sciences and Keşan Yusuf Çapraz Applied Sciences), nine vocational colleges (Edirne Social Sciences, Edirne, Technical Sciences, Edirne Health Services, Keşan, Uzunköprü, Havsa, İpsala, Arda, Tunca), Twenty Research and Application centers (Atatürk's Principles and Revolution History, Balkan, Computer, Plant Breeding, Environmental Issues, Language Education, Cancer Registry, Health, Water Products, Continuing Education, Trakya, Kırkpınar, Women's Issues, Organ Transplantation, International Physics and Applied Mathematics, Education for Mentally and Physically Handicapped Children, Edirne, technology researches, entrepreneurship, distance education) and one kindergarten.