Werner Müller may refer to:
Werner Müller (ethnologist) (1907-1990), German ethnologist and symbologist,
Werner Müller (musician) (1920-1998), German musician,
Werner Müller (canoeist) (born 1922), Swiss canoer,
Werner Müller (politician) (born 1946), German manager and politician, Minister for Economics, see Federal Ministry of Economics and Technology (Germany),
Werner Müller (mathematician) (born 1949), German mathematician,
Werner Müller (referee), Swiss soccer referee, see Estonia national football team 1994,
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