Freedman left Crystal Palace on Tuesday, but talks appeared to have stalled when caretaker boss Jimmy Phillips claimed he would be in charge of the team this weekend.
However, Bolton have now agreed terms with the Scot, but did not specify the length of his contract.
Freedman said: “I am delighted to join Bolton.
"The club is geared up to getting back into the Premier League. There is an impressive setup and structure in place, and a first team squad of undoubted quality.
"I am excited about the challenge ahead of us."
Bolton chairman Phil Gartside said: "Dougie is young and ambitious. When we met his enthusiasm and knowledge of the game was evident.
"He has a real drive and passion, and knows what we want to achieve and how we want to go about it. I am looking forward to working with Dougie to secure that."