The Republic of Ireland Under-21 star spent three months at Hillsborough last season and became an instant crowd favourite.
O'Brien is highly-rated by Trotters boss Sam Allardyce but is not part of his plans at the Reebok Stadium and will cost a nominal fee to bring him across the Pennines.
He captained his last game at Wednesday, the 3-3 draw at Brentford - a thank you gesture by Paul Sturrock for his contribution to the club's great form during his spell.
It is still unclear whether The Owls' move for O'Brien will be a season-long loan switch or a permanent transfer.