The 26-year-old departs the Liberty Stadium club, whose promotion to the Premiership he helped to secure last season, after five years of service.
"I'm delighted to have joined a fantastic club like Bolton," Pratley told the Trotters’ official website. "It was nice to leave Swansea on a high after gaining promotion to the Premier League and I'm now looking forward to showing the fans what I can do here.
"What's important to me is that I join Bolton as a Premier League player after that play-off final. I was delighted to have gained promotion with Swansea. I leave there wishing them well and I'd like to thank everyone there for supporting me.”
"We're delighted to have Darren here. A number clubs were interested in him and we are pleased to have secured his services,” manager Owen Coyle said of his first signing of the summer.
"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 joined the Swans from Fulham in 2006 for a fee of £100,000.