The USA international, 21, moves to Villarreal for a hefty fee, penning a deal to 2032.
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Villarreal are paying an initial €3.2m for Freeman, with a further €2m due in bonuses.
Freeman was recently named MLS Young Player of the Year.
His arrival comes months after the signing of Tani Oluwaseyi, whom Villarreal acquired this past summer from Minnesota United, another MLS franchise.
Villarreal are also the first LaLiga club to sign a player from MLS in Jozy Altidore in 2008.