A total of 13.6m was raised for the new museum, which is due to open in July.
There will be 16 new galleries holding 8000 objects, most of which will go on display for the first time in generations.
There will also be two hands-on discovery centres, a gallery to host international exhibitions and a learning centre.
Sir Angus Grossart, chairman of the board of trustees at National Museums Scotland, said: "I am proud of our tremendous achievement to have not only met, but to have exceeded, our fundraising target.
"The overall ambition of the project has captured the imagination of many supporters to whom we are grateful."
The project is also funded with 17.8m from the Heritage Lottery Fund and 16m from the Scottish Government.