I accept this oddly specific challenge. I'll try to stick to ones you might not have looked into:
I second the Fear Effect games on PS1 and Galaxy Fraulein Yuna on PCEngine, besides those-
Hyper Iria (SNES) - an action/shooter with a pretty cyberpunk aesthetic and settings.
Gourmet Sentai Bara Yarou (SNES) - a very wacky beat-em-up set in the decidedly cyberpunk post-WWIII city of Zeus Heaven Magic in the year 20XX. Mademoiselle is one of the playable characters.
The Ninja Warriors (SNES) - another beat-em-up with cyberpunk elements as well. Kunoichi, one of the 3 characters, is female.
Energy Breaker (SNES) - RPG with definite steampunk elements that might be close enough to what you're looking for.
Battle Golfer Yui (MD) - Off the walls adventure/golf game hybrid. You have to stop an evil scientist who is creating brainwashed cyborg battle golfers.
Life on Earth (MD) - Modern release (2023) for the Genesis/Megadrive. Very cyberpunk shooter with a banger soundtrack, pretty fun.
Ecsaform (PS1) - Interesting SRPG with cyberpunk vibes. Ambitious story (to a fault).
Front Mission 3 (PS1) - TRPG set in a grimy dark mech-filled future. One of the main scenarios focuses on the female character Alisa.
Gunnm: Kasei no Kioku (PS1) - A Battle Angel Alita-based adventure/action RPG game.
Saga Frontier (PS1) - Sci-fi RPG with some cyberpunk elements. There's multiple playable characters to choose from, 2 of them female.
Bubblegum Crash!: Knight Sabers 2034 (PCE) - Simple adventure game set in the Bubblegum Crash! universe. You're a journalist trying to get the scoop on some nefarious goings-on.
Silhouette Mirage (Saturn) - Off-kilter and cartoony action shooter, with a darker cyberpunkish story lurking under the colourful exterior.
Jet Set Radio (Dreamcast) - There, I said it. JSR is cyberpunk. Lots of cool female characters in the playable character lineup!
Maken X (Dreamcast) - Sci-fi/cyberpunk FPS(lasher?). You technically play a sentient sword that "brainjacks" other beings, so... non-binary?
Enemy Zero (Saturn) - Sci-fi, not cyberpunk, but quite an interesting suspense/horror game.
Burning Rangers (Saturn) - Sci-fi game where you play as exo-suit wearing acrobatic jet-pack fire fighters rescuing people in a super high-tech city that has a serious problem with their fire suppression systems.
Chaos Break (PS1) - Fever dream cyberpunkish Resident Evil.
Crisis City (PS1) - Weird sci-fi action game that's trying its best.
Cool, but male protagonist:
Policenauts (Saturn) - Hideo Kojima adventure game screaming cyberpunk, but the protagonist is a dude named Jonathan Ingram.
Shadowrun (MD) - Would be the obvious #1 pick except for the big buff dude as a main character. Cyberpunk as hell and quite fun.
Sakura Wars (Saturn) - Steampunk tactical RPG/dating sim/visual novel, but you're a dude named Ichiro, leader of an all-female magical girl group. Kinda like Charlie's Angels meets Sailor Moon or something.
Psy-O-Blade (MD) - Interesting sci-fi adventure/point-and-click game. Not cyberpunk per se, but might be worth a look. No female protagonist though.
Bit of a stretch in terms of "Cyberpunk", but definitely an interesting sci-fi set-up in Psychic World (SMS). Quite enjoy the MSX2 original as well.
One that I agree with, but, given the somewhat tight criteria, doing our best over here.
I second the Fear Effect games on PS1 and Galaxy Fraulein Yuna on PCEngine, besides those-
Hyper Iria (SNES) - an action/shooter with a pretty cyberpunk aesthetic and settings.
Gourmet Sentai Bara Yarou (SNES) - a very wacky beat-em-up set in the decidedly cyberpunk post-WWIII city of Zeus Heaven Magic in the year 20XX. Mademoiselle is one of the playable characters.
The Ninja Warriors (SNES) - another beat-em-up with cyberpunk elements as well. Kunoichi, one of the 3 characters, is female.
Energy Breaker (SNES) - RPG with definite steampunk elements that might be close enough to what you're looking for.
Battle Golfer Yui (MD) - Off the walls adventure/golf game hybrid. You have to stop an evil scientist who is creating brainwashed cyborg battle golfers.
Life on Earth (MD) - Modern release (2023) for the Genesis/Megadrive. Very cyberpunk shooter with a banger soundtrack, pretty fun.
Ecsaform (PS1) - Interesting SRPG with cyberpunk vibes. Ambitious story (to a fault).
Front Mission 3 (PS1) - TRPG set in a grimy dark mech-filled future. One of the main scenarios focuses on the female character Alisa.
Gunnm: Kasei no Kioku (PS1) - A Battle Angel Alita-based adventure/action RPG game.
Saga Frontier (PS1) - Sci-fi RPG with some cyberpunk elements. There's multiple playable characters to choose from, 2 of them female.
Bubblegum Crash!: Knight Sabers 2034 (PCE) - Simple adventure game set in the Bubblegum Crash! universe. You're a journalist trying to get the scoop on some nefarious goings-on.
Silhouette Mirage (Saturn) - Off-kilter and cartoony action shooter, with a darker cyberpunkish story lurking under the colourful exterior.
Jet Set Radio (Dreamcast) - There, I said it. JSR is cyberpunk. Lots of cool female characters in the playable character lineup!
Maken X (Dreamcast) - Sci-fi/cyberpunk FPS(lasher?). You technically play a sentient sword that "brainjacks" other beings, so... non-binary?
Enemy Zero (Saturn) - Sci-fi, not cyberpunk, but quite an interesting suspense/horror game.
Burning Rangers (Saturn) - Sci-fi game where you play as exo-suit wearing acrobatic jet-pack fire fighters rescuing people in a super high-tech city that has a serious problem with their fire suppression systems.
Chaos Break (PS1) - Fever dream cyberpunkish Resident Evil.
Crisis City (PS1) - Weird sci-fi action game that's trying its best.
Cool, but male protagonist:
Policenauts (Saturn) - Hideo Kojima adventure game screaming cyberpunk, but the protagonist is a dude named Jonathan Ingram.
Shadowrun (MD) - Would be the obvious #1 pick except for the big buff dude as a main character. Cyberpunk as hell and quite fun.
Sakura Wars (Saturn) - Steampunk tactical RPG/dating sim/visual novel, but you're a dude named Ichiro, leader of an all-female magical girl group. Kinda like Charlie's Angels meets Sailor Moon or something.
Psy-O-Blade (MD) - Interesting sci-fi adventure/point-and-click game. Not cyberpunk per se, but might be worth a look. No female protagonist though.
Bit of a stretch in terms of "Cyberpunk", but definitely an interesting sci-fi set-up in Psychic World (SMS). Quite enjoy the MSX2 original as well.
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One that I agree with, but, given the somewhat tight criteria, doing our best over here.
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