Reddit mentions of A Wrinkle in Time: 50th Anniversary Commemorative Edition (A Wrinkle in Time Quintet)

You could try A Wrinkle in Time there is a nice 50th Anniversary edition, and a Boxed Set with the other books to choose from.

Anne Shirley from Anne of Green Gables

Meg Murray from A Wrinkle In Time

Cleo Murphy from The Island Keeper

I know some of these have already been mentioned, so just consider this a second vote for those titles. Also, my list skews heavily towards sci-fi/fantasy, because that is what I tend to read the most of.

By women, featuring female protagonists:

The Handmaid's Tale by Margaret Atwood

Kindred by Octavia E. Butler

The Female Man by Joanna Russ

Kushiel's Dart by Jacqueline Carey

Lavinia by Ursula K. Le Guin

The Circus in Winter by Cathy Day (It's not entirely fair to characterize this as a book about women; it's really a set of interconnected stories featuring both male and female characters. On the other hand, many of the most memorable characters, IMO, are women, so I'm filing it in this category anyway. So there!)

The Protector of the Small Quartet by Tamora Pierce, beginning with First Test (Really, anything by Tamora Pierce would fit the bill here. They're young adult novels, so they're quick reads, but they're enjoyable and have wonderful, strong, realistic female protagonists.)

These Old Shades by Georgette Heyer (Heyer wrote really fun, enjoyable romances, typically set in the Regency period, though These Old Shades is actually Georgian. This one is probably my favorite, but they're really all quite wonderful. Not super heavy stuff, but don't write her off just because of the subject matter. She was a talented, witty writer, and her female protagonists are almost never the wilting "damsel in distress" type - they're great characters who, while still holding true to their own time and place, are bright and likeable and hold their own against the men in their lives.)

A Wrinkle in Time by Madeleine L'Engle (Another young adult book. And, again, I think it's worth noting that L'Engle's books almost always feature strong and interesting female characters. This one is probably her most famous, and begins a series featuring members of the same family, so it's a good jumping off point.)

Persepolis by Marjane Satrapi


By men, featuring female protagonists:

The Last Unicorn by Peter S. Beagle (This is another one that is perhaps not a perfect fit for this category; the titular unicorn is female, but the book is as much about Schmendrick the magician as it is about her. However, there's also Molly Grue, so on the strength of those two women, I'm classifying this book as having female protagonists.)

The Book Thief by Markus Zusak

Coraline by Neil Gaiman (It's a children's book, but there's plenty to enjoy about it as an adult, too.)

By women, featuring male protagonists

Jonathan Strange and Mr. Norrell by Susanna Clarke

The Left Hand of Darkness by Ursula K. Le Guin