Fankhauser is a surname. Notable people with the surname include:

• Clemens Fankhauser (born 1985), Austrian cyclist
• Gerhard Fankhauser (1901–1981), American embryologist
• James Fankhauser (1939–2025), American conductor, tenor and educator
• Merrell Fankhauser (born 1943), American singer, songwriter and guitarist
• Peter Fankhauser (born 1960), Swiss businessman, chief executive officer of the Thomas Cook Group
• Philipp Fankhauser (born 1964), Swiss blues musician and songwriter
• Rupert Fankhauser, Austrian clarinetist
• Urs Fankhauser (1943–2018), Swiss rower