The 22-year-old, who made seven appearances for the Cumbrians at the end of last season, has opted to turn his move from Middlesbrough into a permanent one.
Carlisle boss Keith Curle told the club’s official website: “David comes from a good background with a very good pedigree.
“He started last season in the first-team squad over at Middlesbrough but his game time there was limited because of the situation he found himself in.
“That means we have a player who is hungry to develop and push on.”
Atkinson, who can play anywhere across the back four, also went on loan to Hartlepool last term but did not feature.
Meanwhile, Carlisle have also offered a short-term deal to former Hartlepool defender Nathan Buddle.
The 21-year-old centre-half arrived at Brunton Park on trial from Blyth Spartans in February.