The 27-year-old can play either in defence or midfield strengthens an already strong squad.
Flannigan spent time with Isthmian League Premier Division side Bognor Regis Town during the 2019/20 season on loan from Havant & Waterlooville and then joined the Rocks on a permanent basis in the summer of 2020.
He began his career at Southampton where he featured in the first team.
He has also played at Hampton & Richmond Borough on loan.
Sholing manager Dave Diaper told his club’s website: "Jake is a great player and his quality and experience will be invaluable to us at this level, as we play our first season in the Southern League Premier".
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