The latest ex-Portsmouth man to join League One rivals Wigan's promotion push
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The 42-year-old has been appointed goalkeeping coach at the DW Stadium.
He joins ex-Blues assistant manager Leam Richardson's coaching staff as the Latics plot a promotion push.
So far this summer, Wigan have already snapped up Jack Whatmough and Tom Naylor after their south-coast departures.
Both were offered new contracts to remain at Pompey - but on reduced terms.
As a result, the pair opted against remaining at PO4, with Whatmough penning a two-year deal at Wigan and Naylor signing a three-year contract.
Flahavan spent the 2010-11 season at Pompey but did not make a single appearance, with Jamie Ashdown firmly first choice.
He's the brother of former Pompey keeper Aaron Flahavan, who played more than 100 games for the club before he passed away in car crash in August 2001.