Phil and Kaja Foglio's Girl Genius, Volume 10: Agatha Heterodyne and the Guardian Muse was named 'Best Graphic Story' at the Science Fiction Awards.
Cartoonist Shaun Tan (The Lost Thing, The Arrival) received the award for 'Best Artist'.
Tan has previously won the 'Astrid Lindgren Memorial Award' for excellence in children's literature and an Academy Award for the film adaptation of The Lost Thing, which he also directed.
This is the third year that the 'Best Graphic Story' has been included at the awards, and the third time that Girl Genius has won. Volumes eight and nine have also received the award.
The 2011 Hugo Awards were presented on Saturday night at a ceremony in Reno, Nevada, during the sci-fi convention Renovation.