Cracknell, who played for Boro at Queensgate in 2014 and 2015 as a Hull City loanee, when the Seadogs were managed by Bryan Hughes and Paul Foot, progressed to play for Bradford City and Harrogate Town in the National League and Football League.
The 27-year-old stopper joins Boro after leaving the full-time Football League side this summer.
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Boss Jono Greening said: "A top goalkeeper has been our priority for a number of weeks now.
"When we heard Joe was available, given his quality and reports from his previous spell with the club, his professionalism and attitude matches what we already have in this team.
"Joe still has his best years ahead of him, playing regular football and we are delighted to have Joe between the sticks for next season.".
The keeper rejoins the Seadogs having played alongside Jimmy Beadle, Ryan Blott and Bailey Gooda at Boro and Harrogate Town respectively.