In 1681 he visited Uppsala in Sweden, where he was offered inducements to settle; but his desire for foreign travel led him to become secretary to the embassy which Charles XI sent through Russia to Persia in 1683. He reached Persia by way of Moscow, Kazan and Astrakhan, landing at Nizabad in Dagestan after a voyage in the Caspian Sea; from Shemakha in Shirvan he made an expedition to the Baku peninsula, being perhaps the first modern scientist to visit these fields of eternal fire. In 1684 he arrived in Isfahan, then the Persian capital. When after a stay of more than a year the Swedish embassy prepared to return, Kaempfer joined the fleet of the Dutch East India Company in the Persian Gulf as chief surgeon, and in spite of fever caught at Bander Abbasi he found opportunity to see something of Arabia and of many of the western coast-lands of India.
At Kaempfer's death his mostly unpublished manuscripts were purchased by Sir Hans Sloane, and conveyed to England. Among them was a History of Japan, translated from the manuscript into English by J.G. Scheuchzer and published at London, in 2 vols., in 1727. The original German has never been published, the extant German version being taken from the English. Besides Japanese history, this book contains a description of the political, social and physical state of the country in the 17th century. For upwards of a hundred years it remained the chief source of information for the general reader, and is still not wholly obsolete. A life of the author is prefixed to the History. Kaempfer's original manuscripts are currently kept in the British Museum.