He was born in Oppeln, Silesia into a middle-class German family, which moved to Neisse when he was two years of age. He studied at the universities at Breslau, Königsberg, and Berlin, qualifying as a doctor in 1864. However, he was disqualified from practice, and left Germany for Constantinople, with the intention of entering Ottoman service.
Travelling via Vienna and Trieste, he stopped at Antivari in Albania, found himself welcomed by the European community there and was soon in medical practice. He put his linguistic talent to good use as well, adding Turkish, Albanian, and Greek to his repertoire of western European languages. He became the quarantine officer of the port, leaving only in 1870 to join the staff of Ismail Hakki Pasha, governor of northern Albania, in the service he travelled throughout the Ottoman Empire, although the details are little-known.
When Hakki Pasha died in 1873, Emin went back to Neisse with the pasha's widow and children, where he passed them off as his own family, but left suddenly in September 1875, reappearing in Cairo and then departing for Khartoum, where he arrived in December. At this point he took the name "Mehemet Emin" (Arabic Muhammad al-Amin), started a medical practice, and began collecting plants, animals, and birds, many of which he sent to museums in Europe. Although some regarded him as a Muslim, it is not clear if he ever actually converted.
Charles Gordon, then governor of Equatoria, heard of Emin's presence and invited him to be the chief medical officer of the province; Emin assented and arrived there in May 1876. Gordon immediately sent Emin on diplomatic missions to Buganda and Bunyoro to the south, where Emin's modest style and fluency in Luganda were quite popular.
After 1876, Emin made Lado his base for collecting expeditions throughout the region. In 1878, the Khedive of Egypt appointed Emin as Gordon's successor to govern the province, giving him the title of Bey. Despite the grand title, there was little for Emin to do; his military force consisted of a few thousand soldiers who controlled no more than a mile's radius around each of their outposts, and the government in Khartoum was indifferent to his proposals for development.
The revolt of Muhammad Ahmad that began in 1881 had cut Equatoria off from the outside world by 1883, and the following year Karam Allah marched south to capture Equatoria and Emin. In 1885 Emin and most of his forces withdrew further south, to Wadelai near Lake Albert. Cut off from communications to the north, he was still able to exchange mail with Zanzibar through Buganda. Determined to remain in Equatoria, his communiques, carried by his friend Wilhelm Junker, aroused considerable sentiment in Europe in 1886, particularly acute after the death of Gordon the previous year.
The Emin Pasha Relief Expedition, led by Henry Morton Stanley, undertook to rescue Emin by going up the Congo River and then through the Ituri Forest, an extraordinarily difficult route that resulted in the loss of two-thirds of the expedition. Precise details of this trek are recorded in the daily diaries of the expedition's military commander, Captain William Stairs. Stanley met Emin in April 1888, and after a year spent in argument and indecision, convinced him to leave for the coast, and they arrived in Bagamoyo in 1890.
Emin then entered German service, and led an expedition to the lakes in the interior, but was killed by slave traders at Kinene.