Hermann Minkowski was born in Aleksotas, a suburb of Kaunas, which was then part of the Russian Empire, now Lithuania, to a family of Lithuanian Jewish descent. Hermann was educated in Germany at the Albertina University of Königsberg, where he achieved his doctorate in 1885 under direction of Ferdinand von Lindemann. While still a student at Königsberg, in 1883 he was awarded the Mathematics Prize of the French Academy of Sciences for his manuscript on the theory of quadratic forms. He also became a friend of another German mathematician, David Hilbert. His brother, Oskar Minkowski (1858 – 1931), was a well-known physician and researcher.

Minkowski taught at the universities of Bonn, Göttingen, Königsberg and Zürich. At the Eidgenössische Polytechnikum, today the ETH Zurich, he was one of Einstein's teachers.

Minkowski explored the arithmetic of quadratic forms, especially concerning n variables, and his research into that topic led him to consider certain geometric properties in a space of n dimensions. In 1896, he presented his geometry of numbers, a geometrical method that solved problems in number theory.

In 1902, he joined the Mathematics Department of Göttingen and became one of the close colleagues of David Hilbert, whom he first met in Königsberg. Constantin Carathéodory was one of his students there.

Minkowski died suddenly of appendicitis in Göttingen in 1909.

By 1907 Minkowski realized that the special theory of relativity, introduced by Albert Einstein in 1905 and based on previous work of Lorentz and Poincaré, could be best understood in a four dimensional space, since known as "Minkowski spacetime", in which time and space are not separated entities but intermingled in a four dimensional space-time, and in which the Lorentz geometry of special relativity can be nicely represented. The beginning part of his address delivered at the 80th Assembly of German Natural Scientists and Physicians (September 21, 1908) is now famous:

"The views of space and time which I wish to lay before you have sprung from the soil of experimental physics, and therein lies their strength. They are radical. Henceforth space by itself, and time by itself, are doomed to fade away into mere shadows, and only a kind of union of the two will preserve an independent reality."

David Hilbert's obituary illustrates the deep friendship between the two mathematicians:

Seit meiner Studienzeit war mir Minkowski der beste und zuverlässigste Freund, der an mir hing mit der ganzen ihm eigenen Tiefe und Treue. Unsere Wissenschaft, die uns das liebste war, hatte uns zusammengeführt; sie erschien uns wie ein blühender Garten. Gern suchten wir dort auch verborgene Pfade auf und entdeckten manche neue, uns schön dünkende Aussicht, und wenn der eine dem andern sie zeigte und wir sie gemeinsam bewunderten, war unsere Freude vollkommen. Er war mir ein Geschenk des Himmels, wie es nur selten jemand zuteil wird, und ich muss dankbar sein, dass ich es so lange besaß. Jäh hat ihn der Tod von unserer Seite gerissen. Was uns aber der Tod nicht nehmen kann, das ist sein edles Bild in unserem Herzen und das Bewusstsein, dass sein Geist in uns fortwirkt.

Translated:

Since my student years Minkowski was my best, most dependable friend who supported me with all the depth and loyalty that was so characteristic of him. Our science, which we loved above all else, brought us together; it seemed to us a garden full of flowers. In it, we enjoyed looking for hidden pathways and discovered many a new perspective that appealed to our sense of beauty, and when one of us showed it to the other and we marvelled over it together, our joy was complete. He was for me a rare gift from heaven and I must be grateful to have possessed that gift for so long. Now death has suddenly torn him from our midst. However, what death cannot take away is his noble image in our hearts and the knowledge that his spirit in us continues to be active.

The asteroid 12493 Minkowski and M-matrices are named in his honour.