Gavin Francis collected the £30,000 prize at the Lennoxlove Book Festival yesterday for Empire Antarctica, which describes his 14-month stay as the base camp doctor at Halley on the Caird Coast of Antarctica.
It is described as "the story of one man and his fascination with the world's loneliest continent, as well as the emperor penguins who weather the winter with him".
The 38-year-old, who works part-time as a GP in Edinburgh, has written previous books about his travels and work overseas.
The award judges described Empire Antarctica as "travel writing at its very best", adding that it combines an "evocative narrative with a sublime sensitivity to the natural world".
Francis said: "Winning an award like this, for any writer, is a tremendous endorsement of what it is that they're trying to achieve.
"All 20 books on the shortlist could have been worthy winners which makes me all the more astonished, and delighted, that Empire Antarctica has been chosen as Book of the Year 2013."
The awards, in several categories that also included fiction and poetry, recognise the work of authors from Scotland, who reside in Scotland, or whose book is of particular Scottish interest.