Werner Munzinger (4 April 1832 in Olten, Switzerland – 14 November 1875 in Awsa, Ethiopia) was a Swiss administrator and explorer of the Horn of Africa.
He was born in Olten, and studied science and history at the University of Bern, then later took courses in Oriental studies at Munich University and the Sorbonne. He was the son of Josef Munzinger, member of the Swiss Federal Council.
In 1852 Munzinger arrived at Cairo, where he spent a year improving his Arabic. Entering a French mercantile house, he led a trading expedition to various parts of the Red Sea. Until 1855 he served as French consul at Massawa, when he moved to Keren where he spent the next six years exploring the lands of the Bogos. In 1861 Munzinger joined Theodor von Heuglin in an attempt to explore central Africa, but separated from him in November, proceeding along the Gash and Atbara to Khartoum. There he succeeded von Heuglin as leader of the expedition, and travelled in 1862 to Kordofan, but failed to reach Darfur and Wadai.