Filipp Franz von Siebold is seen as one of the fathers of western style science (or Dutch studies, Rangaku 蘭学) in Japan. He taught medicine, science, botany and more, and was father to the first Japanese female doctor. A memorial to him stands north of Nagasaki close to a school that he founded.

The center is a replica of his house in the Netherlands, and is built on the former location of one of his clinics. Inside one can find items belonging to him, information about his family tree, and his life in general. The museum also covers the Siebold incident, which refers to his banishment from Japan after trying to smuggle maps out of the country. 

After his banishment, Siebold set up the Sieboldhuis in Leiden, where to this day many Japanese artifacts are kept. He left behind his partner and child.