The BBC Wales-produced series, written by Steven Moffat and starring Matt Smith and Karen Gillan, launched with US-set two-part opener 'The Impossible Astronaut' - the first time that Doctor Who had been filmed in the country.
The decision to feature US locations such as Utah and The White House's Oval Office appears to have helped Doctor Who: The Complete Sixth Season top the iTunes US list last year for TV show seasons, ahead of Modern Family and Dexter in second and third.
Moffat, the lead writer and executive producer of Doctor Who, said: "This is incredibly exciting news. It's an honour to be on the same list as all those shows, let alone at the very top. And for a British show to have achieved this in the US is absolutely remarkable. Next, the universe!"
Aired on BBC America, series six of Doctor Who also racked up record TV ratings last year, pulling in almost 1.3 million viewers for the premiere in spring 2011.
The show is one of the BBC's flagship brands, alongside Top Gear, which was the sixth most downloaded show on iTunes in America.
The iTunes (US) Top Ten List of 2011's Most Popular TV Seasons in full:
1. Doctor Who
2. Modern Family
4. Breaking Bad
5. True Blood
6. Top Gear
10. The Walking Dead
Another BBC programme performing well in the US is Sherlock, which is airing on the PBS channel. In the past two weeks, episodes one and two of the show have gone straight in at number one on the iTunes chart in America.
"Coming off the success of BBC America's Doctor Who: The Complete Sixth Season being the #1 downloaded series on iTunes in 2011, it is incredible that Masterpiece's Sherlock: Season 2 hit #1 on iTunes the week it premiered and stays on top today," said Matt Forde, the executive vice president of sales and co-productions at BBC Worldwide Americas.
"Steven Moffat has been turning heads in the US and continues to create amazing television that keeps us all on the edge of our seat," he added.