The gaming industry has always been a bit reluctant with female protagonists. This has a few reasons. One of them is that it is believed the player should identify themselves with the main protagonist and most gamers are believed to be males. I think however it's a misconception that males cannot identify themselves with females though. What does happen to be true is that most gamers appear male, or that has for a long time been the case, but I've seen the number of female gamers grow over time.

There are also games in which the female protagonist is rather a person to lust over than person with an actual personality. However in jRPG where character development and a good story line are pretty important, you can't get away with simply putting in a beautiful girl who triggers the hormones of the male players. Then you need an actual girl with personality, so she can help to carry the story on her shoulders and shape it to her character... well part of it at least.

Most jRPG games do have a male protagonist, but let's list a few here who do have a female protagonist. And there quite often more to these ladies than just being "sexy" (if they are sexy at all).

Virginia Maxwell - Wild Arms 3

In the Wild Arms series Virginia is the very first female protagonist, and in the main series even the only one. (XFire is a kind of a sub-installment and not considered part of the main series). Virginia is a young woman (19 years old during the events of the game) who always dreamed of traveling the world, however she's clueless and naive. This led many Wild Arms fans to hate her, however there is more to her than that. Virginia learns from her mistakes and grows stronger over the course of the game, eventually showing more and more leadership skills over the group she leads (of whom she's the only female). Virginia symbolizes our own devastation when we learn as young people that we live in a cruel world and how we have to grow stronger to earn our place in it.

Terra - Final Fantasy VI

Terra is debatable, as Final Fantasy VI does NOT have an official main character, however, due to the first part of the game circling complete around her, and the fact that she must be present in the final battle against Kefka (and if you don't take her with you, she'll just come to you anyway), not to mention some important plot keys being in her, I'll still consider her for this list anyway.

Terra starts the game in the enemy group, but she merely acts due to being controlled by a kind of tiara that controls her mind. Once she's been freed of that, she doesn't seem to have any recollection of her actions as a soldier. She's guided by some men who quickly discover she can do magic, which makes her quite unique. Terra is a complete stranger to the world and appears to act quite unique due to this. She eventually finds her calling when due to Kefka's crimes many children become orphaned, as she takes care of them as a surrogate mother. It's here that she actually learns to love.

Lightning - Final Fantasy XIII

As I never played this installment of Final Fantasy I'm afraid all I know about her is her name, and how she looks. The reason I added it, is because I'm bound to get a lot of critics when I don't... so here she is!

Yuna - Final Fantasy X-2

Not only Yuna is a female protaganist in this game, but she also leads an all-girl group. Of course, we get to know Yuna first, as the "female sidekick" to Tidus, in Final Fantasy X, where she's tasked to fight Sin. In this game Yuna acts as a very naive, yet very strong girl. Unfortunately her victory over Sin is bitter sweet as it causes Tidus to disappear forever. In X-2 Yuna's cousin Rikku found a clue of Tidus' possible whereabouts and convinces Yuna to walk on her own and join the Gullwings. Yuna completely transforms into a young sexy lady, with a bit more of a no-nonsense attitude, however, at many times she can still show herself the easy to manipulate Yuna. Although Yuna is focused most of all to bring back the man she loves, she still acts as a strong independent woman in X-2... or at least, she tries to.

Ulrika - Mana Khemia 2

Ulrika is one of the two leads in this game, the other being the boy Razeluxe. Mana Khemia is in fact two games in one, and the player can pick to run the story from either Razeluxe's point of view or Ulrika's. Both protagonists have their entire own group, and will even face the other group some times as boss fights. That made that I still added Ulrika to this list.

Ulrika is a lazy, clumsy girl who lacks patience and is therefore pretty impulsive. She quite often needs to be corrected by her friend Chloe. Her rash behavior often gets her into trouble. This easily gets her into conflicts with Razeluxe, although the game hints that the two may actually be in love with each other, although both would rather die than to admit that. Ulrika is not a girl of high standards, causing Lily (a girl in Razeluxe's group) to nickname her "Country Bumpkin".

There is some confusion about Ulrika due to the fact that in the English dub of the game she speaks with a heavy Texan accent, although in the Japanese dub there has not been made any (deliberate) accents.

Now the Atelier series, of which I only played a few games, is one of the few series with more female than male protagonists, but as I haven't played most of those, I'll keep my list to Ulrika. I did leave out Viese Blanchimont from Atelier Iris 2 out on purpose, as her role in the game is too small compared to Felt's role, to hit this list.

Maya - Septerra Core

Maya is a "Junker". She lives on the world of Septerra, and the city and environment where she lives is filled with... well, junk. Maya's people collect everything that is useful from the junk and use it for their own machinery or to do business with. Maya is among the younger generations of junkers the oldest female, making that many young junkers see a kind of a surrogate mother in her.

Interesting to note as that Maya is often target of sexist approaches from male NPC characters, sometimes leading some of her male companions to stand up for her. Maya however appears to be used to this approach, even though she hates it, and manages herself pretty well.

Over the course of the game, she slowly grows into the leader of the group, with even people with a more elitist background taking orders from her. This shows even more Maya is quite capable to manage herself and that she appears to have some leadership skills.

Wendicka Lovejoy - Star Story

Although a main character of my own design, Star Story is based on the Japanese style of RPG creation, and she is a female and she is the main character, so she should be in this list.

Wendicka is a tomboy who was trained to be a space agent for M.E.T.E.O.R. however due to her temper and aggressive nature she messes up, and when this nearly claims the life of her best friend and surrogate sister Crystal, she decides to forfeit her career as a space agent and to be a mechanic in stead. Wendicka is very straightforward and quite often tactless, causing Crystal to say "Oh, Wendicka, don't be so rude". Wendicka is very extremely intelligent though. She manages many machines quite well, has a great interest for "ancient technology" (read the technology we use to day. Star Story takes place in the far future, in the year 3000 to be exact) and is fluent in several alien languages. Although she can appear uncaring, she actually does care a lot about the people around her, and the game will eventually show her softer side.

Wendicka's personality is for a part based on my own... My strong sides and my weak sides. Both have been put a bit more into the extremes. However I made Wendicka a female to make it clear she is not me, and the course of the story is not based on my own life.