Pezeshkian was born in Mahabad, West Azerbaijan, on 29 September 1954 to a Azerbaijani parents. In 1973, he received his diploma and moved to Zabol to serve his conscription duty. It was during this time that he became interested in medicine. After completing his service, he returned to his home province, where he entered medical school and graduated with a degree in general medicine. During the Iran–Iraq War (1980–1988), Pezeshkian frequently visited the front lines, where he was responsible for sending medical teams and working as a fighter and doctor. He finished his general practitioner course in 1985, and started teaching physiology at the medical college.
After the war, Pezeshkian continued his education, specializing in general surgery at Tabriz University of Medical Sciences. In 1993, he received a subspecialty in cardiac surgery from Iran University of Medical Sciences. He later became a specialist in heart surgery, leading him to become president of Tabriz University of Medical Sciences in 1994, a position he held for five years.