Simon Milne, currently chief executive of the Scottish Wildlife Trust, will become only the 16th person to hold the post since it was created in 1699.
Milne was also previously director of the Sir Harold Hillier Gardens in Hampshire for four years, preceded by a distinguished 20-year career as a Royal Marines officer.
Chair of RBGE Board of Trustees Sir Muir Russell said: "I am delighted to have someone of Simon’s calibre joining us to continue the excellent work done by Steve Blackmore.
"Simon is familiar with many of the issues facing us, particularly our hot topics of conservation and biodiversity, and we will benefit hugely from his extensive experience in senior leadership roles. I very much look forward to working with him in the future."
Milne said he was thrilled to be offered the opportunity to take up such a prestigious and important role, adding: "I had a fulfilling and enjoyable time leading the Scottish Wildlife Trust, it was an honour to work with so many committed staff, volunteers and members to help protect and restore our precious wildlife and wild places.
"The role of Regius Keeper at the Royal Botanic Garden Edinburgh offers me an opportunity to return to the remarkable world of plants. I am looking forward with relish to new challenges and the opportunity to play a crucial role in developing appreciation, education, knowledge and conservation of the plant kingdom."
The RBGE's four gardens at Edinburgh, Benmore, Logan and Dawyck attract nearly a million visitors each year. Milne will take up his new post in February.