After his return to Iran in 1961, he joined Nemazee Hospital in Shiraz as an attending surgeon and became an Associate Professor of Surgery at Pahlavi University School of Medicine in Shiraz where he established a General Surgery Residency Program. He became Chief of Surgery at Saadi and Nemazee Hospitals in Shiraz and Professor of Surgery at Pahlavi University School of Medicine in 1963. Farrokh Saidi was the Dean of Medical School, Pahlavi University School of Medicine during 1968–1969. Again, he returned to Boston to complete a two-year fellowship in Pediatric Surgery at Massachusetts General Hospital. He moved to Tehran in 1972 and was Chief of Surgery at Hossein Fatemi Hospital, Rey, and subsequently Chief of Surgery at Bank Melli Hospital, both in Tehran, Iran. In 1985, he joined Shahid Beheshti University of Medical Sciences as a Professor and Chief of Surgery, and established the Thoracic Surgery Fellowship program at Modarres Hospital in Tehran. During 1974–1975 and before the Iranian revolution, Farrokh Saidi served as the Under-Secretary for Medical Education and Health Services of the Minister of Education, Abdol-Hossein Samiy. He has been a permanent member of the Iranian Academy of Medical Sciences since 1990. He has been a Fellow of the Third World Academy of Sciences since 1987. Farrokh Saidi has published extensively on surgical treatment of hydatid cyst and esophageal cancer. In the early-mid 1990s, he founded the Iranian Society for the Study of Esophageal Cancer and conducted a few studies on esophageal cancer targeting one of the highest incidence cancers in the World in northeast Iran. Farrokh Saidi is currently a Professor of Surgery Emeritus at Shahid Beheshti University of Medical Sciences and practices general and thoracic surgery at Iran-Mehr Hospital in Tehran.
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In November 1992, Farrokh Saidi, together with some 1,700 world's leading scientists, including the majority of Nobel laureates in the sciences, issued an appeal and warned that human activities inflict harsh and often irreversible damage on the environment and on critical resources and suggested a great change in our stewardship of the earth and the life on it, is required. This appeal was written and spearheaded by Henry Way Kendall, former Chair of Union of Concerned Scientists. In a correspondence to the Nature in December 2009, he was among thirteen prominent Iranian academicians who deplored the cases of alleged plagiarism by Iranian scientists. The authors believed Iranian culture places an excessive emphasis on the value of academic credentials, both for advancement in official professions and in social standing and especially, Iran's political class has an unusual affinity for possessing academic distinctions and this accounts for a disproportionate share of academic fraud in this group.
