Makoto Kobayashi is born in Nagoya to physician Hisashi Kobayashi and his wife Ai Kaifu. In 1945, Kobayashi’s family is evacuated to Kawagoe Village in Mie Prefecture to escape the aerial bombardment over Nagoya during World War II. Shortly after the war the father dies and Kobayashi and his mother find their house in Nagoya burned. They move then in his mother's family house.

Makoto Kobayashi visits CERN for three months. While he is there the W particle is discovered.

Makoto Kobayashi, together with Toshihide Maskawa, conducts researches on chiral symmetry at Nagoya University. In March 1972 Kobayashi receives his doctoral degree in physics.

Makoto Kobayashi and Toshihide Maskawa predict the existence of at least three families of quarks, the subatomic particles that are the constituents of protons and neutrons, and thereby provide the foundation for the principle of broken symmetry. In 1975, the tau lepton is discovered. This finding indicates the existence of third-generation quarks.

Makoto Kobayashi enters the Physics Department of Nagoya University where he begins his research in particle physics as a member of Prof. Shoichi Sakata's laboratory. There he meets Toshihide Maskawa, with whom he begins a longlasting collaboration.

Makoto Kobayashi is appointed Professor of the Institute of Particle and Nuclear Science and therefore he is directly responsible for the Institute's experimental research activities including those conducted using the B-factory accelerator. In 2003 he becomes Director of Institute of Particle and Nuclear Studies and in 2006 is appointed Professor Emeritus.

Makoto Kobayashi becomes Assistant Professor at the National Laboratory of High Energy Physics in Tsukuba Science City getting involved in the Tristan collider project. In 1985 he becomes Professor. In 1989 he is designated as the Head of Physics Division II and is responsible for the experimental study groups, planning the accelerator after Tristan.

Makoto Kobayashi becomes Research Associate in the Physics Department of Kyoto University. There, he works with Maskawa on CP violation, namely, the violation of the combined conservation laws associated with charge conjugation C and parity P in weak interactions.

Makoto Kobayashi receives one fourth of the Nobel Prize in Physics along with Toshihide Maskawa "for the discovery of the origin of the broken symmetry which predicts the existence of at least three families of quarks in nature". The other half is awarded to another Japanese theoretical physicist, Yoichiro Nambu, "for the discovery of the mechanism of spontaneous broken symmetry in subatomic physics."

Makoto Kobayashi becomes Executive Director of Japan Society for the Promotion of Science (JSPS).