Walker has made 29 appearances for Colchester on loan this season after also enjoying a spell with the League One club last term.
The 22-year-old, who did not make a first-team appearance for Chelsea, has now agreed a long-term deal with Colchester to the delight of manager Joe Dunne.
"I'm delighted that we've signed Sam for the next 18 months," Dunne told the club's official website.
"He is another young and hungry footballer who has decided to come here and play, which is great testament to what we are doing here at Colchester United.
"He has done fantastically well for us over the past year but he is still improving and will get even better in the right environment for development.
"He will certainly have that here and he has a great support network, with our goalkeeper coach George Bankole and the other keepers he works with every day."