The man, who cannot be named, was arrested at Springfields Academy in Calne in October 2013.
Wiltshire Police said they carried out a "complex investigation" but said no criminal charges would be brought.
A Crown Prosecution Service spokesman said there was "insufficient evidence to provide a realistic prosecution".
A man who was arrested after a child was seriously injured at a special school in Wiltshire will not face charges after the case was dropped.