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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