Jean Sulpice won the coveted award a year after taking over L'Auberge du Pere Bise, a century-old hotel on the shores of Lake Annecy which has played host to the likes of Winston Churchill, Charlie Chaplin and Richard Nixon.
Gault & Millau's owner Come de Cherisey praised Sulpice for his lightning rise through the rarefied world of French cuisine.
“He is working his way up a high mountain pass,” he told AFP.
On his website Sulpice describes his food as being “filled with the riches of the mountains” where he grew up.
His menu gives pride of place to regional products, such as venison, brown trout and Beaufort cheese.
Sulpice ran a two-star Michelin restaurant in Val Thorens ski resort — Europe's highest — before snapping up the property on Lake Annecy, 100 kilometres (62 miles) to the north, in 2016.
After a facelift costing several million euros the stately Auberge reopened to the public in May.
Among the other winners of Gault & Millau's 2018 awards were 32-year-old Cedric Grolet of the five-star Le Meurice hotel in Paris, named the country's top pastry chef.
Born in the Loire region to a truck driver father and hairdresser mother Grolet has gained a huge following on Instagram for his colourful, fruity creations.
Gault & Millau publishes an annual guide of 3,800 eateries across France, over two-thirds of which offer dishes costing under 30 euros ($35).
It is less well-known than the Michelin guide, whose stars are seen as a sort of culinary holy grail.