The history of Chiba University School of Medicine dates back to 1887, when the Chiba Public Hospital, a prefectural institution with medical teaching facilities, was founded. After several name changes, in 1923 its status was raised from Chiba Medical College to Chiba Medical University. The Department of Legal Medicine was established as a specialist department in 1928.

After the end of the Second World War, it became Chiba University School of Medicine with the establishment of Chiba University in 1949, and Yunosuke Kagaya was appointed as the first Professor of Legal Medicine. He was followed by Professor Yoshinosuke Miyauchi as the head of department in 1960, and Professor Yasushi Kimura in 1971. Professor Kimura made numerous appearances in the media, authored a book on bloodstain testing, and contributed a written opinion to the retrial of the Fukawa Case, helping to exonerate the defendants.

When Chiba University Hospital was rebuilt in 1980, the School of Medicine moved into the old hospital. This historical building, constructed in 1937, remains the campus of the School of Medicine today. In 1991, Professor Masahiro Kiuchi was appointed as the fourth head of department. When the graduate school was reorganized as the Graduate School of Medicine in 2001, the Department of Legal Medicine was incorporated into the graduate school, which is its current status.

In 2003, Professor Hirotaro Iwase joined Chiba University from the University of Tokyo and was appointed as the fifth head of department. In 2004, the department rented a CT vehicle to carry out its first CT scans and pointed out the limitations of purely visual external inspections. In the same year, Chiba University and other national universities were reorganized as independent corporations, and funding for legal medicine was cut throughout the national university sector. However, in 2006 it became possible for expenses such as the cost of testing to be defrayed by the police. The department therefore purchased a used CT vehicle, and further improved its equipment by purchasing a 16-row helical CT scanner, and installing a liquid chromatography tandem mass spectrometer (LC/MS/MS) in 2009, bringing it closer to international standards for investigating cause of death.

When Professor Iwase was first appointed, the number of autopsies stood at around 150 cases per year; however, by 2012, this had risen to 362. The staff of eight (including one graduate student) in 2003 has also tripled to 24 (including six graduate students) in 2014. A team of eight doctors, three dentists, one pharmacist, and seven clinical laboratory technicians makes the Center the largest university department of legal medicine in Japan. It still faces many challenges, however, including the small number of full-time employees, and cramped facilities.