The restaurant topped Harden’s “Top 100 Best UK Restaurants” list, which was based on 30,000 reports from 3,000 diners.
Leith trio The Kitchin, Restaurant Martin Wishart, and The Little Chartroom reached fifth, 14th, and 31st respectively.
In Glasgow, Cail Bruich finished in 50th spot, with Unalome by Graeme Cheevers in at number 68.
The Peat Inn and The Cellar, both in Fife, took 76th and 99th.
Andrew Fairlie died four years ago this month, with the restaurant being run by head chef Stephen McLaughlin and general manager (GM) Dale Dewsbury since his death.
They were part of the team that launched the venue in 2001, with McLaughlin becoming head chef in 2006, and Dewsbury taking over as GM in 2012.
Peter Harden, co-founder of Harden’s, said: “Andrew Fairlie may sadly no longer be with us, but his spirit lives on in this restaurant [that] bears his name.
“Reaching the top spot this year is a huge credit to his long-time lieutenants, head chef Stephen McLaughlin and GM Dale Dewsbury.”
McLaughlin added: “While it is always an honour to receive commendation for the restaurant, the fact that Harden’s Top 100 is diner-led is a special honour and a particular testament to the hard work of the full team to ensure every guest has the best possible experience when they dine with us.
“This time four years ago, we were dealing with the terrible loss of our wonderful friend and mentor, Andrew Fairlie, and committed to maintain his incredible legacy.
“I’m extremely proud that we’re here today achieving these fantastic accolades.
“People knew Andrew as a champion of great food and service, and this ethos remains the same.
“We have a fantastic, talented team who are all invested and continue to be driven to maintain – and exceed – the standards set by Chef Andrew.”