After finishing his Doctor of Philosophy (1979) at Kyushu University, Japan, he was Associate and Assistant Professor at the University of Texas at Houston for 4 years (1979–1983). He was also Visiting Assistant Professor at Washington University in Saint Louis (1985, 1986) and Visiting Fellow at the Imperial Cancer Fund (Imperial Cancer Research Fund) in London (1989).
He has also been co-appointed as the Special Consultant of the National Institute of Advanced Industrial Science and Technology (AIST), as a Visiting Professor of Keio University, University of Tokyo, and Tokyo Institute of Technology and as a Visiting Director of Rikagaku Kenkyūsho. He is the Founding Editor of the journal Genome Biology and Evolution, the Executive Editor of the journal Gene, Academic Editor of Federation of European Biochemical Societies Letters, Associate Editor of Molecular Biology and Evolution and PLOS Genetics, and Section Editor of Computer Genomics in Business Service Management Genomics. He has served on the editorial boards of 6 international journals. Previously he was the Editor of Journal of Molecular Evolution for 8 years (1995–2003).
He is leader of the Japanese team of the H-Invitational international consortium who was tasked with creating a database linking the 21,037 validated human genes to their biological function.
Gojobori has worked extensively on the rates of synonymous and non-synonymous substitutions, positive selection, horizontal gene transfer, viral evolution, genome evolution, and comparative gene expression. In recent years, he has focused on the evolution of the brain and Central nervous system.
Gojobori has served as the Program Director of the Council for Science and Technology Policy (CSTP) of the Government of Japan and is the Science Officer of the Ministry of, Science, Sports, Culture, and Technology (Ministry of Education, Culture, Sports, Science and Technology). He has contributed to the DDBJ/GenBank/European Molecular Biology Laboratory database construction as well as the H-Invitational human gene database.
Fellow: American Association for the Advancement of Science, American Academy Arts and Sciences (foreign) (honorary). Member: International Society Molecular Evolution (vice chair since 1994), Genetics Society Japan (treasurer 1988-1990, council board 1993-1994, home secretary since 1995, advisory board since 1996), Society Molecular Evolution, Swiss Institute of Bioinformatics.
Married Mariko Gojobori. Children: Jun, Yoko.