Bolton narrowly missed out on a play-off place but Freedman's side had an impressive April that included four wins, a draw and a single defeat.
Freedman narrowly pipped Charlton's Chris Powell and Brighton boss Gus Poyet to the monthly gong.
Speaking about Freedman's win, award panel member Alan Curbishley said: "It was a great month for Dougie Freedman which resulted in an end-of-season surge for his side, who only just missed out on a play-off place.
"I am sure Bolton will be in contention again next season in what will be his first full season in charge."
Bournemouth boss Eddie Howe was named the npower League One Manager of the Month after he steered the Cherries into the Championship.
Howe's side missed out on the title but had a month to remember, winning four and drawing just the once to ensure a near-perfect finish to the season.
Nigel Worthington took the League Two award after York City remained unbeaten in April with four wins and a draw from their last five fixtures to ensure they remained in the division next season.