I found a few which may count.
>When Marnie Was There
>Anna, a shy 12-year-old girl, is sent to spend time with her aunt and uncle who live in the countryside, where she meets Marnie. The two become best friends. But Anna gradually discovers that Marnie is not quite who she appears to be.
>Fuse Teppō Musume no Torimonochō
>Hamaji is a girl who lives alone in the mountains, surviving as a hunter just like her grandfather. One day she receives a letter from her brother Dousetsu who lives in Edo. Reaching the big city, she gets lost and ends up meeting Shino, a fusé who helps her in finding her brother's house. Dousetsu wants to team up with her to win a bounty award to hunt down the fusé, which are people who are part wolf and part human that eat other people's essence.
>Like the Clouds, Like the Wind
>Ginga is a simple—yet energetic—country girl, living with her father far from the capital city of the empire. When she learns of an opportunity to become a concubine of the young new Emperor, with the possibility of getting a regular food supply in the bargain, Ginga convinces her father to let her go. Once there, she meets all of the other potential head wives, each of whom have various reasons for being there. All of them must learn to read and write, learn the history of their country, and learn the proper mannerisms for being in the royal court.
>City Hunter (multiple films)
>The series follows the exploits of Ryo Saeba, a "sweeper" who is always found chasing beautiful girls and a private detective who works to rid Tokyo of crime, along with his associate or partner, Hideyuki Makimura.
>One day, Hideyuki is murdered, and Ryo must take care of Hideyuki's sister, Kaori, a tomboy who becomes his new partner in the process. However, Kaori is very susceptible and jealous, often hitting Ryo with a giant hammer when he does something perverted. The story also follows the behind-the-scenes romance between Ryo and Kaori and the way they cooperate throughout each mission.
>Haikara-San: Here Comes Miss Modern
>Raised by a single father who is also an army general, Benio is a tomboy with qualities that are deemed not feminine, and proclaims herself to be a modern woman. Her grandmother sets her up in an arranged marriage with an army lieutenant Shinobu Ijuin. Benio strongly believes that women should have the right to choose their own husband and wants a marriage based on love. She makes it her mission to give Shinobu's family a bad impression so that the arranged marriage doesn't go through. However, this becomes difficult as she starts falling for Shinobu's charm.
There was also The Girl Who Leapt Through Time, which we already watched. In truth it would be a lot easier to post shows that prominently feature tomboys.