Bruce Minto was hailed for “outstanding leadership in the arts” at the annual Oscars-style ceremony celebrating joint projects between the cultural and business sectors.
Mr Minto has spearheaded fundraising campaigns which have generated more than £20 million for the Edinburgh-based attraction, which is currently the most popular in Scotland.
He was at honoured at the Arts & Business Scotland Award at the 30th annual Royal Concert Hall in Glasgow.
Among the other winners were National Theatre of Scotland fundraisers Elly Rothnie and Stella Litchfield, who were honoured for their efforts for the company in its first decade.
Mr Minto, a founding partner of the Edinburgh legal firm Dickson Minto, was appointed to lead the development board of the museum in 2007 before being appointed chair in 2012.
His tenure has coincided with two multi-million pound overhauls of the museum, which celebrated its 150th anniversary last summer, when 10 new art, design, science and technology galleries were unveiled.
The most recent project, which saw 3000 objects from the museum collection go on display, many for the first time in a generation, helped the museum topple Edinburgh Casle as the country's busiest attraction, with 1.81 million visitors, up 13.4 per cent on the previous 12 months.
Last week the National Museum of Scotland was named best attraction at VisitScotland's annual Thistle Awards for the tourism industry.
Mr Minto said: “It is a wonderful organisation, tremendously well led by (director) Gordon Rintoul and his team.
"There are hundreds of people putting in amazing effort, skill, drive, commitment and expertise - the deep knowledge in that organisation is terrific to see.
"I'll keep going for a wee while longer, I think. The people around me are so inspiration - it's very hypnotic and enticing to remain part of it as it's such a great organisation."
FULL LIST OF WINNERS
Elly Rothnie and Stella Litchfield, National Theatre of Scotland
Check-It Scaffold Services
Glasgow City Council & Art Pistol
Deloitte & National Theatre of Scotland
Auchindrain for The Runrig Project
MacRoberts LLP & The Cumnock Tryst
Scottish Environment Protection Agency & Right Lines Productions
IFS Worldwide & Cultural Documents