The news will provide some cheer to Sir Richard Branson’s airline, which has appeared to have all the cards stacked against it since going into battle with BA on the route a year ago.
The figures also revealed Edinburgh as the UK’s third most punctual main airport after London City and Birmingham, with average delays of 9.2 minutes.
Glasgow was fifth, after Stansted, with 10.3 minutes.
Passengers on Virgin’s “Little Red” flights were delayed by an average of 5.7 minutes compared to 13.8 minutes for BA passengers to the notoriously-congested main London airport.
The growing route is used by 1.3 million people a year.
Virgin is also now Edinburgh’s most punctual, since the only two carriers with shorter delays last year, Minoan Air and BMI Regional, have since scrapped their routes to the airport.
Virgin has had an uphill battle against its former bitter adversary since effectively replacing BMI on the Edinburgh-Heathrow route after the airline merged with BA.
It has far less frequent flights from Edinburgh than BA and a much smaller route network at Heathrow for transfer passengers.
Virgin customers also have to change terminal at Heathrow while most BA passengers enjoy direct connections from terminal five.
However, Virgin’s superior punctuality will be valued by people just flying to London, who account for three in four of its passengers. The airline said the proportion was growing.
The figures, compiled by the website flightontime.info from official Civil Aviation Authority statistics, cover 3,146 Virgin flights since their launch last April.
BA said the vast majority of its 10,500 Edinburgh flights covered by the figures over the whole year were to Heathrow, with some to Gatwick.
The airline said punctuality had suffered from knock-on delays by its aircraft also flying on other routes, including in Europe.
Its spokesman said: “We understand the importance of punctuality to our customers and we have been working hard to improve the service.
“During the first two months of 2014 we have seen a marked improvement, and we will aim to maintain this throughout the year.”
Joe Thompson, director of network and alliances for Virgin Atlantic said: “Customer feedback has been excellent since we launched Virgin Atlantic Little Red last year and we recognise punctuality and reliability play a big part in this.
“Passengers flying short haul are always time-conscious whether they are connecting to a long-haul flight, heading to a meeting or catching the last flight home.
“We work extremely hard to ensure our flights depart and arrive on time and it’s great to see Little Red’s excellent punctuality is being recognised.”
Edinburgh Airport chief operating officer David Wilson said: “We’re delighted with these new figures, which show Edinburgh Airport as the largest in the top three.
“Last year was a phenomenal year for our airport. Our collaboration with our business partners and continued focus on customer service has ensured we were the most punctual airport in Scotland and show we are striving to maintain and improve our standards during a period of rapid change.”