As the most recent JoJo's Bizarre Adventure: Stone Ocean series demonstrated, shonen anime with a female protagonist can be done and done well while following typical shonen conventions and tropes. The title might seem like an oxymoron at first, given that shonen manga is specifically aimed at teenage boys, as are its derivative anime.
Though they are few and far between, anime originating from shonen work with female protagonists have indeed graced the screens of anime fans before. More would always be welcome, but the circumstances tend to be very specific for this approach to truly work. Below are some of the best examples from MyAnimeList of shonen anime that center on a female protagonist.
Tokyo ESP (2014) - 6.55
Tokyo ESP is your typical superhero story of an unsuspecting character obtaining powers. The anime ran for 12 episodes in the 2014 summer season and was based on its manga, which ran on Monthly Shonen Ace. It focuses on Rinka Urushiba, a part-time waitress and high school student whose everyday life is interrupted when she gains extrasensory perception powers.
As her father is a former cop, she has been instilled with a strong sense of justice. So she unwillingly goes on to become Tokyo's hero with her new powers. As she gains notoriety, she draws the attention of an organization that has questionable goals and strong powers and fighters in its ranks.
Medaka Box (2012) - 7.03
Medaka Box took the idea of a Goku-type character, made it female, and cranked the power levels of everyone up to over 9,000. One of its villains is amongst the strongest in all anime, receiving the ability to will for the diminishment of other characters' existence.
The series is a huge allegory for shonen manga as a whole, making use of the tried and true tropes of the genre while breaking the fourth wall with a refreshing degree of self-awareness. There is some discussion to be had about whether it is Medaka or Zenkichi that is the true protagonist, but Medaka's importance to the plot made this series stand out during its Shonen Jump run because of her presence.
Shikabane Hime (2008 - 2009) - 7.21
Shikabane Hime is set in a world in which dead girls battle monsters in order to gain access to heaven. The organization of this is conducted by a somewhat shady group known as the Kougon Cult. Makina Hoshimura becomes contracted to a monk in this cult to be a part of this battle after being brutally murdered along with her family.
Throughout the series, Makina ends up in situations narratively fitting for a shonen protagonist. From tragic beginnings, she has to quite literally fight her way through her enemies to achieve peace. Her enemies are recognizable and, later on, have a special name: the Seven Stars.
Kakegurui Seasons 1 & 2 (2017 - 2019) - 7.26
Kakegurui is set in the luxurious Hyakkaou Private Academy, where the children of the rich and wealthy decide their fates by the games and gambles they play. A great majority of the cast is female, but it is Yumeko Jabami who serves as the lead. Audiences are just like Ryota Suzui, the exceedingly likable male lead of Kakegurui, who is in place to watch as Yumeko is unleashed on the unsuspecting students.
Yumeko shows a range of emotions throughout the series, from disgust and unhinged to exceedingly polite and outright savage. This ties into her love for gambling and how she experiences it. It is very refreshing to see such varied emotions in a female character, especially since, as the protagonist, they do not discredit her intelligence at any point.
Soul Eater (2008 - 2009) - 7.48
Soul Eater's partnership-focused premise of meister-plus-weapon allowed it to be fairly unique in the anime landscape of the late 2000s. While Soul may have been the weapon, the one wielding it and depicted as fighting was Maka Albarn. A lot of what she goes through reflects the same trials and tribulations most commonly seen in male protagonists.
And yet the creator was sensitive to the fact that it was a female lead with her own personality. Maka and Soul Eater continue to be one of the most popular 2000s shonen series for the uniqueness of the world, story, and narrative perspective they contributed.
Patlabor (1989 - 1990) - 7.68
Patlabor is a classic in the world of anime. It is, in fact, considered to be one of the best animated movies of the '90s. Serialized as a manga in Weekly Shonen Sunday at the same time as the anime was airing, the manga went on to win the 36th Shogakukan Manga Award for shonen in 1991. The main character is Noa Izumi, a member of the Tokyo Metropolitan Police Special Vehicle Section 2, Divison 2.
In an alternate timeline, robots known as Labors have taken over a lot of work in Japanese society. The police use Patrol Labors, or Patlabors, to combat crimes, terrorism, and issues involving other Labors. Noa is the best pilot in her division. She shows affection to them as she did her pets, and this allows her to get more out of her Labors, constantly placing her in the middle of the action.
Claymore (2007) - 7.75
The synopsis of Claymore is very similar to that of The Witcher: creatures killing people throughout a country, a select group of warriors that can kill these creatures, and townspeople that are terrified of these warriors but need them. The differences are that the warriors are women and that they are named Claymores. There are more differences, of course, but Clare's life as a Claymore definitely shares a lot with Geralt's story.
In the 2000s, Claymore stood out as a story in which the majority of its fighting force was female. While almost all shonen series at the time had female characters that contributed to the battles and overall plotlines, few had their female leads front and center like Claymore.
The Ancient Magus Bride (2017 - 2018) - 8.07
The Ancient Magus Bride is a unique, magical love story. The protagonist, Chise Hatori, sells herself at a human auction in her search for a permanent home. She ends up being bought by Elias Ainsworth, who reveals he is a magus and wants to make her his bride. Neither of them quite knows what love is, and a large part of the series is dedicated to the two of them discovering it.
This gorgeous love story is framed with magic and action sequences as Chise learns about the world she is now inhabiting, and how special she is. This anime has something for everyone: a slow-burn romance, a journey of self-love, British fae and fairies, magic, and battles - and it is all explored from the viewpoint of Chise, the female lead.
JoJo's Bizarre Adventure Part 6: Stone Ocean (2021) - 8.41
Stone Ocean was always going to rank near the top as the most recent example of a female-led shonen anime. The sixth part of Hirohiko's story had JoJo's newest incarnation as a girl incarcerated for a crime she did not commit in a jail in Florida. JoJo is a shonen through and through, and Jolyne Kuujou is part of a long dynasty that would not be able to avoid joining the fight.
Like any shonen protagonist from other parts of the same manga or any other shonen manga, Jolyne awakens her latent powers and then becomes embroiled in a larger, world-ending battle. As shonen protagonists do, Jolyne has the charisma to draw others to her cause as friends and allies from the most unlikely circumstances.
The Promised Neverland Season 1 (2019) - 8.54
The first season of The Promised Neverland was groundbreaking. The story of the Grace Field House orphans trying to survive when the odds are incredibly stacked against them drew interest and awe from viewers, and in the center of this struggle for survival is Emma, an 11-year-old girl that serves as one of the leaders of the orphans.
One of the earliest characters to find out the truth about their seemingly idyllic life, Emma very quickly decides that things cannot remain as they are and that they must act to save all the children. Her agency and role as a female lead really stand out in this series, as her decisions carry the most amount of weight.