JH Williams III, W Haden Blackman and Amy Reeder's DC Comics title has been named 'Outstanding Comic' by the Gay and Lesbian Alliance Against Defamation.
This is the second win for the character, whose run in Detective Comics received the same award in 2010.
The title was selected from a shortlist featuring Avengers: The Children's Crusade, Secret Six, Veronica Presents: Kevin Keller and X-Factor.
"This is extremely gratifying, because we've been working very hard to make this character multifaceted and someone to believe in, while showing her develop realistic personal relationships over time," Williams wrote on his blog.
"So the recognition from the GLAAD awards bolsters us greatly. And thank you for all of the support the series has been getting from you all, the comics readership community."
The awards honour positive portrayals of the LGBT community across the arts that "inspire change".
Reeder recently announced that she is departing Batwoman over "creative differences".