Obata was born and raised in San Francisco. Due to his family’s Japanese heritage, he was nearly interned with other Japanese-Americans during World War II. Though his family was sent to an internment camp, he avoided it by leaving the School of Architecture at the University of California-Berkeley to study architecture at Washington University in St. Louis, the only university in the United States willing to accept Japanese nationals at that time. He earned his bachelor of architecture degree there in 1945.

He then studied under master Finnish architect Eliel Saarinen at the Cranbrook Academy of Art in Bloomfield Hills, Michigan, receiving his master’s degree in architecture and urban design in 1946.

After serving in the U.S. Army from 1946–1947 and working as an architect in the Chicago office of Skidmore, Owings and Merrill from 1947–1951, Obata returned to St. Louis in 1951 to join the firm of Minoru Yamasaki, designer of the World Trade Center towers. Four years later, in 1955, he joined architects George Hellmuth and George Kassabaum in establishing the St. Louis-based architecture firm Hellmuth, Obata and Kassabaum.

In 2010, Obata was featured in a book written by Marlene Ann Birkman and published by The Images Publishing Group titled, Gyo Obata: Architect | Clients | Reflections. The book features 30 of Obata’s projects (and clients) spanning five decades.