The city has raced up from fourth place in 2009, when the last survey was carried out, to second behind Newcastle and ahead of Manchester and Belfast.
Glasgow finished sixth, up from joint 11th three years ago. London remained in 18th place out of 20. Nottingham, the previous winner, slipped down the table to joint 12th.
The survey was carried out by Runner's World magazine, which describes itself as the world's best-selling running publication.
It said: "Running is thriving in the Scottish capital, thanks to the successful Jog Scotland initiative, the annual Edinburgh Marathon Festival and the council's Activcity project which aims to make Edinburgh the most physically active city in Europe by 2020."
Bob Johnson, secretary of Edinburgh-based Carnethy Hill Running Club, which has 300 members and was established almost 30 years ago, said: "Edinburgh is a fantastic city for runners.
"We've got the Pentland Hills nearby – we have a big hill-running scene around Scotland.
"There are running events in the Meadows and we have lots of running shops that are very keen about putting events on.
"We find a certain percentage of our runners are injured because they run off-road, so we have a cycling section going as well.
"Cycling in Edinburgh is a massive thing, too."
The two-day Edinburgh Marathon Festival celebrated its 10th anniversary in May when a record 23,000 runners from more than 100 countries set off from the heart of the city to tackle the UK's fastest marathon course.
Among them was 101-year-old Fauja Singh, from Ilford, east London, the world's oldest marathon runner, who crossed the line in five hours and 23 seconds, as part of a four-man relay race team known as Sikhs in the City.
As well as the relay, the events included a full marathon, a half marathon, a 10K, a 5K, and junior races.
The festival is second in UK marathon size only to London. Entries are now open for the 2013 event, which takes place on May 25 and 26.
Nigel Holl, chief executive of scottishathletics, which runs the Jog Scotland programme, said: "We're delighted to hear Jog Scotland is making such a difference.
"Close to 25,000 people are part of Jog Scotland across the country and we have a large number of very active groups in Edinburgh.
"Our supportive programmes are designed to make getting fit an enjoyable experience for people of all abilities. The aim is not only to increase the number of people running, but make sure they have a great time doing it, and stick with it for the long-term."
Councillor Richard Lewis, Edinburgh City Council's convener of culture and leisure, said: "Edinburgh has exceptional running routes with fantastic built and natural backdrops such as Arthur's Seat.
"We've also been really successful in attracting a wide range of running events to the capital.
"We work hard with partners through our Activcity programme to make Edinburgh an attractive city for runners of all abilities."
Contextual targeting label: