Based on a 2012 Mustang GT, the vehicle was inspired by the US Navy Blue Angels aerobatics display team.
It sold at the Experimental Aircraft Association's (EAA) 2011 Air Venture Oshkosh meet on July 29, with the $400,000 going towards the EAA Young Eagles organisation, which has helped more than 1.2m youngsters learn to fly since 1992.
The car was decked out in the same blue and gold that adorn the Blue Angels' F-18 Hornet aircraft, and featured the team's name and insignia both inside and out.
One-off vehicles are highly valued by collectors looking for that unique model for their garage.
This model has the potential to become a modern-day classic in years to come, such is the affection for unique Mustangs with car collectors.
In 2009, famed car collector Tammy Allen bought a No 5 Iacocca Silver 45th Anniversary Edition Mustang for $352,000 at a Barrett-Jackson sale.
Ford has been producing Mustangs since 1964.
Edsel B Ford II, a member of Ford's board of directors, commented: "The precision, discipline and excitement that define the US Navy's Blue Angels flight team are qualities we celebrate at Ford.
"With this project we take great pride in continuing our support for EAA and the Young Eagles organisation".
One-off Mustang auctions are becoming a tradition with the EAA.
In 2008, Ford offered its AV8R model for the auction, inspired by the F-22 Raptor stealth fighter.
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