It was due to the initiative taken by the government of Alexandros Papanastasiou that the Aristotle University of Thessaloniki was founded in 1925. The Aristotle University initially consisted of five faculties: that of Theology, Philosophy, Law, Medicine, and Physics and Mathematics. The Faculty of Physics and Mathematics opened its doors in 1927, consisting of the School of Physics, the School of Mathematics, the School of Chemistry, and the School of Natural Sciences.
 
The School of Pharmacy was founded in 1955, as part of the Faculty of Physics and Mathematics of the Aristotle University of Thessaloniki (Government Gazette Α′ 226, 24-8-1955), with just twenty students initially being admitted. The faculty staff was composed of ten professors and four senior lecturers – six of them were members of the teaching personnel of the Faculty of Physics and Mathematics and five of them of the Faculty of Medicine.
 
Initially, two Chairs were founded: a) the Chair of Pharmaceutical Chemistry, with aspects of Pharmacognosy, and b) the Chair of Pharmaceutical Compounding and Pharmaceutical Technology. Moreover, two laboratories were established: a) the Laboratory of Pharmaceutical Chemistry, with aspects of Pharmacognosy, and b) the Laboratory of Pharmaceutical Compounding and Medicine Control, which were initially part of the Faculty of Physics and Mathematics (Government Gazette Α′ 205, 12-10-1957).
 
Constantinos Makris was the first professor who taught pharmaceutical courses in the School of Pharmacy, such as Pharmacognosy, Pharmaceutical Chemistry and Pharmaceutical Compounding. In the 1970s, and after the retirement of Constantinos Makris (1968), pharmaceutical courses were taught by professor Georgios Fokas (Pharmacognosy and Pharmaceutical Chemistry) and by professor Nikolaos Oikonomou-Petrovic (Pharmaceutical Technology-Prescription Compounding).
 
In 1983, the two laboratories were incorporated into the School of Pharmacy, pursuant to the ministerial decision no. Β1/107 (Government Gazette Β′ 73, 24-2-1983). Moreover, pursuant to the ministerial decision no. Β1/211 (Government Gazette Β′ 92, 8-3-1983), two departments were established: the Department of Pharmaceutical Chemistry and the Department of Pharmaceutical Technology, along with the corresponding laboratories. In 1983, pursuant to the presidential decree no. 130 (Government Gazette Α′ 57, 3-5-1983), the School of Pharmacy was incorporated into the Faculty of Human Sciences. In 1985, the Department of Pharmacognosy-Pharmacology was established, pursuant to the ministerial decision no. Β1/780a (Government Gazette Β′ 689, 15-11-1985). Two years later, the Laboratory of Pharmacognosy and the Laboratory of Pharmacology were founded (pursuant to the presidential decree 491 & 492, Government Gazette Α′ 227, 23-12-1987) and were incorporated into the corresponding department.  In 1997, the Laboratory of Pharmaceutical Analysis was founded as part of the Department of Pharmaceutical Technology, pursuant to the presidential decree no. 232 (Government Gazette Α′ 175, 1-10-1997). The curriculum of the Departments of the School of Pharmacy and the studies that make up its content was determined pursuant to the ministerial decision no. Β1/676 (Government Gazette Β′ 27, 19-1-1987). In 2004, the Senate decided to abolish the Faculty of Human Sciences (presidential decree no. 247, Government Gazette Α′ 235, 30-11-2004). Only the School of Pharmacy has retained its status as an independent school.
 
Until 1989, the School of Pharmacy was located on the 3rd floor of the building of the School of Chemistry. In 1989, it was transferred to the building of the new wing of the Faculty of Sciences, where it is still located, occupying three floors.
 
Every year 110 to 150 students enroll in the School of Pharmacy. Currently, there are about 700 students in the School and the pharmaceutical courses offered are taught by eight tenured professors, six associate professors, three assistant professors and two lecturers. Non-pharmaceutical courses are taught by faculty members of the School of Chemistry, the Faculty of Medicine, the Faculty of Veterinary Medicine, the School of Mathematics, the School of Physics and the School of Biology.
 
The graduate studies programme of the School has been in operation since the academic year 2001-2002, offering specialization in various areas of pharmacy and leading to MA and PhD degrees.