Season 1 of Jubei-chan the Ninja Girl: Secret of the Lovely Eyepatch premiered on April 6, 1999.

Yagyu Jubei was Japan's greatest swordsman. His skill was legendary, but the one enemy he couldn't conquer was death. Before he died, though, he gave his disciple hope - there would be a successor, and this deserving person would receive all the power and skill of Yagyu Jubei, along with the Lovely Eyepatch.

After 300 years of searching, the disciple finds Nanohana Jiyuu, a rather ordinary girl who has just moved to a new town and started going to a new school. As if going to a new school weren't stressful enough, now Jiyu is told that she is heir to the legendary talents of Yagyu Jubei. And she will have to put those talents to good use and stop the assassins of the rival clan!

Season 2 of Jubei-chan the Ninja Girl: Secret of the Lovely Eyepatch premiered on January 8, 2004.

One day on her way to school, Jiyuu unexpectedly runs across Koinosuke. In his hand, Koinosuke holds the Lovely Eyepatch. When Jiyuu arrives in school, a transfer student has come to her class, her name is Yagyuu Freesia, her eyes are clear blue and she is supercute.