The 33-year-old made 33 National League appearances for the Shrimpers in 2021-2022, having previously played in excess of 150 games for the club between 2013 and 2017.
Having started out at Hull City, Atkinson also counts the likes of Bradford City, Mansfield Town and Port Vale as former clubs.
"We are delighted to have completed the signing of Will," reflected United manager Paul Cox. "Understandably, he was much sought after following his time at Southend and we are delighted to have him onboard.
"He is an intelligent footballer, who is not only technically excellent, but also brings an experienced mindset into our midfield."
Atkinson is the Pilgrims' seventh new signing – following Ben Pollock, Lebrun Mbeka, Ellis Myles, Jordon Crawford, Alex Brown and Scott Pollock.