The former Rochdale and Macclesfield midfielder originally joined the club on a non-contract basis last February.
But despite interest from other clubs, Flitcroft was keen to make the move a permanent one and he will be a key player for manager Graham Barrow next season.
Flitcroft is the fourth player at Gigg Lane to accept new terms after Jon Cartledge, Simon Whaley and Steven Maden.
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