Ishiguro was born in Nagasaki, Japan, on 8 November 1954, the son of Shizuo Ishiguro, a physical oceanographer and his wife Shizuko. At the age of five, Ishiguro and his family left Japan and moved to Guildford, Surrey, as his father was invited for research at the National Institute of Oceanography (now the National Oceanography Centre). He did not return to visit Japan until 1989, nearly 30 years later, when he was a participant in the Japan Foundation Short-Term Visitors Program.