She takes over from Ken MacQuarrie, who recently took up the newly-restored UK-wide post of BBC director nations and regions.
Ms MacKinnon will become the senior editorial figure with responsibility for BBC Scotland content across radio, television and online.
BBC Director General Tony Hall said he had "no doubt Donalda will be a great success in the role".
He added: "She's been the driving force behind a great range of programming - and has been responsible for so many ambitious partnerships for us.
"She's also an outstanding mentor and manager."
Ms MacKinnon, who was previously the Head of Programmes and Services for BBC Scotland, will take up her new position immediately and will be based at Pacific Quay in Glasgow.
She said: "Being part of the huge team effort that brings so many different programmes to all our audiences is a real privilege and I'm delighted to have the opportunity to help shape that even more in the future.
"The new Charter offers great opportunities - and a few challenges - as we aim to make great content that reflects Scotland's diversity and distinctiveness for audiences here, across the UK and the world.
"I know there's a wealth of talent and creativity in BBC Scotland, in the wider sector and in partner organisations. Working brilliantly together, I'm confident we can make compelling and enthralling programmes that entertain and inform all of our audiences."
Donalda MacKinnon has been appointed the new Director of BBC Scotland.