Shishido Tamaki was born the third son of Naotsugu Yasuda, who was a feudal retainer of the Choshu clan in 1829. Tamaki's childhood name was Tatsunosuke. His real name was Shisei, which was later changed to Keiu. Tamaki studied in the private school of Bunnoshin Tamaki (Shokason-juku) together with Shoin Yoshida and others, and also studied in the domain school Meirinkan. In 1848 Tamaki was adopted by Taika Yamagata, a Confucian scholar who worked for the domain, and called himself Hanzo. In 1854 Tamaki made a round of inspection of Ezochi (roughly corresponding to present-day Hokkaido island), Sakhalin, and the Russian Empire, accompanying Norimasa Muragaki: a government official in the Edo bakufu (the last feudal government headed by a shogun). The following year Tamaki went to Nagasaki to study. Around that time Tamaki began to get to know men of noble ideals in many domains, and was appointed the head student in Meirinkan when he returned to the domain in 1857. He taught Sadahiro (later to become Motonori) Mori, who was the heir of the domain there. In 1860 Tamaki followed Sadahiro to Edo and was active in national affairs. In 1862 Tamaki and Genzui Kusaka who were both from the same domain, plus Shintaro Nakaoka from the Tosa Domain, along with others, visited a scholar, Shozan Sakuma, who had confined himself in the Matsushiro Domain.
They offered Shozan a post in the Choshu Domain, but it never came to fruition However they learned about the international situation and theories of national defense from Shozan. After returning to his domain the following year, Tamaki started to visit domains in the Kyushu area advocating the Sonno Joi theory (supporting reverence for the Emperor and the expulsion of foreigners). After the August 18 Coup of the same year, Tamaki went undercover in the Kyoto and Osaka areas to observe the situation.
The Choshu clan were still promoting Sonno Joi, but they ran into problems due to their defeat in the Hamaguri Rebellion (Kinmon no Hen in Japanese) and the attack on Shimonoseki by the four countries' combined fleet. The allegiance faction (the conventional party) won control of the Choshu clan and consequently Hanzo was confined. However Shinsaku Takasugiand Hirobumi Ito and others took up arms, which changed the opinion of the clan again, resulting in Hanzo being pardoned. However the bakufu (feudal government headed by a shogun) decided to dispatch an interrogator to the Choshu Domain. The Choshu clan forced Hanzo Yamagata to change his name to Bingonosuke Shishido and become an adopted child of the Shishido family (who provided the chief retainer of the domain) and made him meet Naoyuki NAGAI, the interrogator from the bakufu, in Kokutai-ji Temple in Hiroshima (Hiroshima City). As the negotiation took such a long time, Tamaki was taken into custody in the Hiroshima Domain. However when the Second Conquest of Choshu occurred the following year, Tamaki was released to compensate for the defeat of the bakufu. In recognition of his achievements during the period, Tamaki was allowed to establish a new branch family of Shishido and was also appointed jikimetsuke-yaku (a kind of supervisor post).
After the Meiji Restoration, Tamaki became "gon daisanji" (second to governor) of the Yamaguchi Domain in 1869. The following year Tamaki moved to Tokyo and became "gyobushoyu" (Junior Assistant Minister of Justice) in October. In November 1871 Tamaki became "shiho-taifu" (a high post in the Ministry of Justice). In 1872 he became "monbu-taifu" (a high post in the Ministry of Education). In 1877 he became a councilor of the Senate. In March 1879 Tamaki was appointed the minister plenipotentiary to Qing. This was immediately after Ryukyu Domain was abolished and Okinawa Prefecture had been established (the Ryukyu Annexation) and Ryukyu's sovereignty had become an issue between the two countries. Shishido submitted a memorandum to the Foreign Office in Qing written by Munenori Terashima and Kaoru Inoue, the foreign minister, which stipulated the legal basis of Japan's territorial right to Ryukyu. In the following year, the negotiations ended with agreement. However due to opposition by Hung Chang LI, senior vassal in the Qing dynasty, the agreement was not sealed and Tamaki broke off the negotiations and returned to Japan in January 1881.
In the year following his return to Japan, Tamaki started serving the Imperial Household Ministry and in April 1884 became a member of "Sanjiin" (one of the old ministries and agencies mainly related to the executive and legislative branches). In December 1885 Tamaki became a councilor of the Senate again. In May 1887 he was given the title of viscount in recognition of his achievement to date. In 1890, at the inauguration of the Imperial Diet, he was appointed a member of the House of Peers and became "kinkeinoma-shiko" (a title in the Imperial court).
Tamaki died in October 1901 at the age of 73.