The Scot's award was announced at the Barclays-sponsored LMA annual awards dinner in Nottingham.
The award is voted for by the entire LMA membership and takes into consideration the performance of all managers during the season, based upon all the resources available to them.
It completes a double for Ferguson, who also won the Premier League award.
All the awards were presented by England head coach and LMA president Fabio Capello.
Ferguson has won the main award once before, in 1999, when he took United to a Champions League, Premier League and FA Cup treble.
He succeeds Reading boss Steve Coppell, who won the award in both of the previous two seasons.
Ferguson said: "It is a tremendous honour that my fellow managers and LMA members should deem me worthy of this award. I am very proud to receive it."
The winner of the Coca-Cola Championship manager of the year award was West Brom boss Tony Mowbray after steering Albion to the title and promotion.
Swansea manager Roberto Martinez won the League One award, and Graham Turner lifted the League Two award after taking Hereford to automatic promotion in their first season back in the Football League.
LMA chairman Howard Wilkinson said: "The awards recognise the achievements of the managers across the four top leagues in England.
"Recognition by your peers is an incredible privilege and this year's winners should be proud of their achievements.
"The LMA would like to congratulate all the managers for playing such an integral role in another fantastic season."
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Showing comments 1 to 8 and replies | View All
edinburgh red, edinburgh (13/05/2008 at 11:01)
Deano58 (13/05/2008 at 11:24)
Duncan, London (13/05/2008 at 12:12)
bobbydazzler (13/05/2008 at 12:16)
Lord Ruud (13/05/2008 at 12:16)
Justin The Great, manchester (13/05/2008 at 12:22)
ON TOP OF THAT HOW MANY MUPPETS HAVE BEEN SLATING SAF CALLING FOR HIS HEAD IN RECENT YEARS
WE SHUD PUT UP A STATUE OF HIM OUTSIDE O.T.
I RECON DAVID MOYES SHOULD GET RUNNER UP HES DONE A GREAT JOB YEAR IN YEAR OUT TO COMPETE WITH THE TOP GUNS HES A SHADOW MANAGER
tooth&claw, manchester (13/05/2008 at 15:03)
Duncan, London (13/05/2008 at 16:53)