This trilogy (The Golden Compass/Northern Lights, The Subtle Knife, The Amber Spyglass) is usually talked about because of it’s anti-religion stance, but it is also very pro-women (part of the reason Pullman wrote it was as a direct response to C. S. Lewis’ treatment of Susan in the Narnia series).
Without giving too much away, the story follows a young girl named Lyra, who lives in an alternate universe parallel to our own, on a journey to the North and back and forth through multiple universes as she comes of age.
Most of the main characters are girls/women.
Lyra – young girl, protagonist
Mrs. Coulter – an antagonist, but like many of the adult characters in the trilogy it isn’t as black and white as it seems
Serafina Pekkala – a witch queen and friend to Lyra
Dr. Mary Malone – a physicist from our universe