The award was presented to the singer by basketball star Kobe Bryant in the ceremony at The Forum in Los Angeles, which honours achievements across all areas of entertainment.
Timberlake, 35, referenced boxing great Muhammad Ali in his speech and urged teenagers to “be part of the solution, not part of the problem”.
He said: “Muhammad Ali fought in the ring, but he fought for peace, too. And he became the heavyweight champion of the world because, as we all know, he could float like a butterfly and sting like a bee.”
The SexyBack star also said he hoped his one-year-old son, Silas, “watches this one day”, adding: “Go out, do the impossible and become the greatest generation yet.”
Timberlake has won a total of 23 Teen Choice Awards during his career, and earlier this year presented Bryant with an Icon Award at a major sporting awards ceremony.
The award coincides with the 10-year anniversary of his 2006 album FutureSex/LoveSounds.
British boyband One Direction were also honoured with a few surfboards, the Teen Choice Awards trophy of choice, as they were named Choice Song Group winner for their hit Home, as well as taking the Choice Fandom and Choice Music Group awards.
Big winners in the movie arena included Captain America: Civil War, which was named Choice Movie Sci-Fi/Fantasy winner and its star, Chris Evans, also took home Choice Movie Actor in the same category for his role as the superhero.
Oscar winner Jennifer Lawrence was named the winner in the Choice Movie Actress Sci-Fi/Fantasy category, as well as Choice Movie Actress winner.
Brooklyn Beckham attended the show with his girlfriend Chloe Grace Moretz who was named the winner of the Choice Movie Actress Comedy category.
In TV, teen drama Pretty Little Liars was the stand-out winner with four awards.
Hollywood actress Jessica Alba led a poignant tribute to the many Americans whose lives have been affected by gun violence in the country.
Alba took to the stage with a group of teenagers to honour the lives lost in recent tragedies such as the Orlando nightclub massacre.