The Expanse series has Naomi Nagata, Avasarala, Bobbie Draper, and Drummer (among others)

The Revelation Space trilogy by Alastair Reynolds has the badass Ilia Volyova (cyborg space pirate; it makes sense in context lol) as a main character (not primary protagonist though) in the first two books and Ana Khouri (ex-military/assassin) is the primary protagonist in the second two (and major character in the first).

Some of Reynolds's other works also have strong female protagonists as well (e.g. Pushing Ice and the whole Revenger series). House of Suns is one of my favorites, and there are two protagonists, male and female, and have equal spotlight throughout.

Both of those are hard sci-fi, so hopefully that's your jam.

Try out the Wayfarer's series! Becky Chambers is amazing. Her books are wholesome and character focused, and give you a great feel of what it would be like living in that setting.

I also really like Brandon Sanderson's Cytoverse. It's a fantastic adventure that will keep surpsing you, but it is YA, so be ready for a little silliness.

Parable of the Sower by Octavia Butler.

• Silo series by Hugh Howie
• Shatter Me by Tahereh Mafi (Young adult dystopian scifi)
• Across the Universe by Beth Revis (Young adult)
• Bird Box by Josh Malerman (apocalyptic thriller)
• Mistborn by Brandon Sanderson (fantasy, not scifi, but I'm digging up stuff from when I used to read more prolifically)
• Revelation Space series by Alastair Reynolds. I read this so long ago, and I feel like their were some great female characters, but I can't remember if any were the protagonist. Each novel shifts around.

The Space Between Worlds vy Micaiah Johnson

A Half-Built Garden by Ruthanna Emrys

Pretty much anything by Octavia Butler.

Pretty much anything by Cherie Priest, the Clockwork Century books are great!

Gideon the Ninth?

Takes like 5 chapters for it to find it's feet but it's lesbian necromancers and swordfighters in space with a very snarky point of veiw character.

It's kind of more scifi fantasy but a good time.

The "Broken Earth" series by N.K Jemesin

First book

Xenobiologist Kira Navárez in To Sleep In A Sea Of Stars might not win feminist awards, but I really liked her, the world building and the story. IIRC, it was relatively clean of overly sexist BS.

Echoing what others have already said here: The Expanse. The depth and quality of pretty much all the main characters is great. And there are several fantastic female characters who are strong, smart, and wonderfully written.

The Steerswoman series by Rosemary Kirstein, and the Merchant Princes series by Charles Stross—both series that may not seem like sci-fi at first, but become increasingly so as they progress.

I see lots of good picks here, a few of my favourites books mentioned... I love The Expanse in particular, but "Pushing Ice" by Alastair Reynolds had a better focus on complex female characters.

I thought YT was a well written character in Snow Crash. She took no shit from anyone.

Sassinak by Anne McCaffrey was pretty good.

Seveneves, tho it is written by a dude. Great characters tho.

Artemis by Andy Weir might be a good match.

Vatta’s War series by Elizabeth Moon is solid. Starts just a tad slow but ramps up quickly into action. I reread it every other year or two.

The Iron Widow by Xiran Jay Zhao. Think Neon Genesis Evangelion X Female Rage X Chinese History. It's by no means a perfect book, but it's entertaining, the premise is very interesting and the character work is quite good!

Well my first recommendation was going to be Ancillary Justice, but there’s also Artemis by Andy Weir! It’s been a minute since I’ve read it but I don’t immediately recall it snacking of a “men writing women” feel.

Edit: Not super SciFi, but like steampunk fantasy maybe… Another option might be Mistborn by Brandon Sanderson.

Second Edit: Whatever you do DONT read Hyperion. Oof that one was one of the most ridiculous examples of “men writing women” I have read, although he notably grew as the series progressed.

The Bel Dame series by Kameron Hurley is good. It starts with God's War.

I liked the Academy/Priscilla Hutchins series by Jack McDevitt. Character drama isn't necessarily a big part of it, partly because most people act like real humans (for sci-fi) and it's more about the space exploration angle and, on the series level, about how that changes over time.

Pushing Ice by Alastair Reynolds

Look, at this point I'm basically just "That guy who recommends the Luna books", but this is yet another situation where they really are the right answer. Luna: New Moon is your starting point. The series is absolutely bursting at the seams with diverse and interesting female and non-binary characters. It also features some wonderfully atypical male characters who really play around with our understanding of what it means to perform masculinity. I am obsessed with Lucas Corta, iron fisted patriarch whose one weakness is for the beautiful young man who plays bossa nova for him, and I'm equally obsessed with his son Lucasino, the rich kid playboy who has fucked his way through his entire friendship circle, and loves makeup, androgynous clothes and baking.

Anyway, Luna: New Moon by Ian MacDonald. Give it a look.

“The Chanur Saga” by C. J. Cherryh is full of great female leads!

Very fun series that works under a premise of first contact from the alien perspective.

Would fantasy fit the bill? If so I can recommend The Warden and Necrobane by Daniel Ford.

I had so much fun reading The Adventures of Amina al-Sirafi by Shannon Chakraborty. It is squarely in the fantasy genre. Not SciFi like you're asking for. But I can't recommend it enough.

Amina is a very rare character: she is simultaneously an older woman, a single mom, a pirate, a lover, and a legendary hero. Chakraborty does an admirable job of balancing all these different aspects of her main character's personality. The story is bombastic and fun, the supporting characters are charming, the setting is historical and fantastic all at once. This book is incredible, I could not put it down.

I have heard good things about the audio book. I read it in text form though, so I can't confirm that myself.

Honor Harrington or Safehold by David Weber.

Less scifi and more fantasy, I just finished The Priory Of The Orange Tree and I highly recommend

And just want to add A Great And Terrible Beauty as another Fantasy book that is a wonderful read (series)