Fraser died aged 57 in his post at Tokyo and was buried on 6 June 1894 in the foreigners' section of the municipal cemetery at Aoyama in central Tokyo. With a ceremonial procession arranged by the British architect Josiah Conder, the coffin was carried out of the British Legation at 3.00 pm, and reached St. Andrew's Church, Shiba Koen at 4.00 pm. Many mourners came to pay their respects, including Japanese government ministers and all the Foreign Representatives. The funeral service and committal were conducted by the Bishop Edward Bickersteth.