Fukuda studied administration engineering at Keio University, graduating in 1974 and earning a master's degree in 1976.
He began doctoral work in the same field, but in 1976 transferred to the University of Waterloo to their PhD program in combinatorics and optimization.
[3] After completing his PhD, he returned to Japan as an assistant professor at the Tokyo Institute of Technology.
In 2008 he gave up his position at the École Polytechnique Fédérale de Lausanne, becoming affiliated only with ETH Zurich, and since 2012 he has held a joint appointment in mathematics and computer science at ETH Zurich.
With Tamás Terlaky, Fukuda worked on a particular class of pivot algorithms, known as the criss-cross method.