The winning programme, All Different, All Beautiful, works with 13- to 19-year-olds in schools, hostels and community settings in areas of high deprivation. The sessions are run over five days.
The judges felt the programme successfully got the sexual health message across in a non-medical way.
Kai Wooder, Brook Wirral's education manager, said: "Innovation can be tricky as it often involves taking a few risks but the rewards can be fantastic, as winning this award has shown."
The other joint winner was Education for Choice, an education charity that helps young people make informed decisions about abortion.
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