Professor Christopher Breward will take over from Dr Gordon Rintoul at the helm of the Edinburgh attraction, which dates back more than 150 yesrs, in April.
His job will also involve running the National Museum of Flight in East Lothian, the National War Museum at Edinburgh Castle and the National Museum of Rural Life, in Lanarkshire.
Professor Breward has spent the last two and a half years at the National Galleries of Scotland in a new role as director of collection and research.
A former head of research at the V&A design museum in London, he was the first principal of the art school in the wake of its merger with Edinburgh University in 2011
It was announced in August that Dr Rintoul would be stepping down in March after an 18-year tenure, which included overseeing an £80 million transformation of the museum which had helped it become the busiest visitor attraction in Scotland. The project was completed earlier this year.
Bruce Minto, chair of the NMS trustees, said: "Chris’s background and experience make him ideally placed to lead National Museums Scotland as we build upon our successes and embark upon the next phase of development of our museums and collections.
"He brings a fresh perspective to our remarkable multi-disciplinary collection, and the vision and ability to further extend our profile and reach, both nationally and internationally, through new creative connections and collaborations. We all look forward to welcoming him."
Professor Breward said: "Museums have become crucial spaces of connection, inspiration and the promotion of knowledge and understanding.
"I look forward with great excitement to working with the trustees, staff, audiences, partners and supporters in making the very best of Scotland’s exceptional collections, across its five physical sites and in the digital realm, so that through compelling displays and programming we can explore the big ideas and tell the important stories that will make a difference nationally and across the world in the coming decades."