The 26-year-old became a free agent after the Welsh club promotion to the Premier League but manager Brendan Rogers had said he was keen to keep hold of the player.
Bolton were able to make a move on the midfielder after he rejected a new contract with the Welsh side, and manager Owen Coyle is thrilled to have brought the player to the Reebok Stadium.
“We're delighted to have Darren here. A number clubs were interested in him and we are pleased to have secured his services,” Coyle told the club’s official website.
“He's an exciting player, who has the right character to blend into our squad. He is a good addition as we look to progress our club further in the upcoming season.”
Pratley spent five years at Swansea, making 199 appearances and scoring 31 goals.
His final outing for the club was in their promotion-winning playoff final against Reading.
He came through the youth system at Fulham, playing alongside current Wanderers players Zat Knight and Sean Davis.
He was loaned out to Brentford on two occasions where he was able to play regular football before his permanent switch to south Wales in 2006.