Scottish architect Gareth Hoskins’ firm won the Andrew Doolam award for the best building in Scotland for 2011.
The museum, which re-opened in August following a £47 million overhaul, has welcomed hundreds of thousands of visitors to its new galleries.
Hoskins was also presented with a £25,000 prize.
The award was presented by Culture Minister Fiona Hyslop at a ceremony in the Scottish Parliament last night. Ms Hyslop said: “The transformation of the National Museum is truly breathtaking, making this project a worthy winner.”