The 22-year-old enjoyed a loan spell with the Us last season and has now switched to the Weston Homes Community Stadium on a permanent basis.
"I think it's a great deal for the supporters particularly and the club in general," manager John Ward told the club's official website.
"We are delighted to have Freddie on board and I think that three years is a commitment from him to us and what we are trying to achieve here.
"He wants to do it with us and that's a massive thing and as soon as he was released from West Ham, Freddie wanted to come here and I was wanting him to come.
"I think it says a lot about us - he sees the new training ground, he sees the senior group as a close knit one who want to work together."