Werner Müller-Esterl (born 13 July 1948) is a German biochemist who served as president of the Goethe University Frankfurt from 2009 to 2014.

He obtained his medical license in 1979 and his habilitation in clinical biochemistry in 1985.

He was director of the Institute for Biochemistry II and the Gustav Embden Center for Biological Chemistry from 2000.

His research focuses on the molecular mechanisms that control the cardiovascular system.

[4] In October 2008 he was elected president of the Goethe University.