Johann Alexander Ecker (10 July 1816 – 20 May 1887) was a German anthropologist and anatomist born in Freiburg im Breisgau. He was the son of Johann Matthias Alexander Ecker (1766–1829), a professor at the University of Freiburg.
He studied medicine at the University of Freiburg as a pupil of Karl Heinrich Baumgärtner. He received his medical doctorate at Freiburg in 1837. In 1840 he started work as a prosector at the University of Heidelberg, where during the following year, he became a privat-docent. At Heidelberg, his influences included Friedrich Tiedemann, Friedrich August Benjamin Puchelt, Theodor Ludwig Wilhelm Bischoff and Maximilian Joseph von Chelius. In 1844 he became a full professor at Basel, later returning to Freiburg as a professor of physiology and comparative anatomy (1850). In 1870 he was co-founder of the Akademische Gesellschaft.
As an anthropologist, Ecker conducted excavations of early burial sites in the Kaiserstuhl region of southwestern Germany. At the University of Freiburg, he created a museum of anthropology and ethnography (Museum für Urgeschichte und Ethnographie). With prehistorian Ludwig Lindenschmit the Elder (1809–1893), he founded the first German journal of anthropology, the Archiv für Anthropologie.