Returning to physics, in 1952 he worked with Werner Heisenberg in Göttingen and in 1954 with Wolfgang Pauli in Zürich.

In 1964 he founded in the city, together with Abdus Salam, the International Centre for Theoretical Physics (ICTP).

In the same year he promoted the Advanced School of Physics, which in 1978 was upgraded to the International School for Advanced Studies (SISSA), the first Italian higher education institution providing doctoral degrees (besides the Scuola Normale Superiore in Pisa), and became its first director.

In his autobiography L'arcipelago delle meraviglie, published in 2000, Budinich pleads for a reunification between science and philosophy and suggests the superior capability of mathematics to explore unknown paths of scientific discovery.

His main work, The Spinorial Chessboard, written together with the Polish mathematical physicist Andrzej Trautman, refers to Élie Cartan's conceptual foundation of spinor geometry and explores its applications to modern physics.