Born in 1796 to a medical family in Würzburg, Germany. He studied medicine and natural sciences at the University of Würzburg, joined the Dutch army as a military physician, and via Java arrived in Japan in 1823 as physician at the Dutch factory on Dejima in Nagasaki. In 1824 he opened the private academy Narutaki-juku on the outskirts of Nagasaki, teaching Western medicine to more than fifty Japanese students including Takano Chōei, Itō Genboku, and Ninomiya Keisaku. He energetically studied Japanese flora, fauna, geography, and folklore and introduced them to Europe. In 1828, when maps of Japan by Inō Tadataka and other prohibited items were found among his luggage before his return, the 'Siebold Incident' erupted and he was expelled from the country. After the Japan-Netherlands Treaty of Amity and Commerce he returned in 1859 and stayed until 1862. He died in Munich in 1866. Father of Kusumoto Ine.

Combining a scientist's restless curiosity with an educator's passion. He held a deep love for Japan, treating its culture and nature not with disdain but as objects of study on equal footing. At the same time, the ambition to spirit away forbidden maps reveals another side — the very type of the 19th-century European intellectual living in the space between science and adventure.

From Siebold's Narutaki-juku emerged the leading figures of late-Edo Western medicine — Itō Genboku, Takano Chōei, Ninomiya Keisaku, and others — who laid the foundations of modern Japanese medicine. His Fauna Japonica, Flora Japonica, and Nippon, which he introduced to Europe, became classics of Japanese studies in the West. Memorial sites honoring him stand in Japan, Germany, and the Netherlands — the Siebold Memorial Museum in Nagasaki, SieboldHuis at Leiden University, and others. His daughter Ine became Japan's first female obstetrician, and his line, too, contributed to the history of Japanese medicine.