The Chelsea youngster spent the second half of last season on loan at the Community Stadium, making 19 starts and keeping nine clean sheets as he played a big part in helping the Essex outfit avoid relegation from League One.
And boss Joe Dunne has moved to bring the 21-year-old back to the club on an initial deal which runs until mid-January.
"Sam did extremely well for us when he was here last time around and he was someone we wanted back for the new season," Dunne told Colchester's official website.
"We have great competition for places now in goal - they will push each other and bring the best out of each other."
Walker will challenge Mark Cousins and youngster Shaun Phillips for United's number one spot.