The 22-year old was in his second loan spell with the League One club but has now penned a permanent long-term deal at Colchester Community Stadium.
"I'm delighted that we've signed Sam for the next 18 months," U's boss Joe 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."
Walker has made a total of 48 appearances for the U's which includes 26 starts this campaign.
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