1-year-old Kenichi Mitsuba is an average kid who goes to secondary school and struggles with his studies, he is very stubborn and is very lazy and therefore always ends up frustrating his parents and teacher. He loves to find an easy way of things much to the annoyance of Hattori.
Meanwhile, a little ninja named Hattori Kanzo befriends Kenichi. Hattori is now a part of the Mitsuba family along with his brother Shinzo, and his ninja dog, Shishimaru. Hattori helps Kenichi with his problems, and constantly keeps an eye on him, as a good friend. Yumeko is portrayed as Kenichi's love interest.
The main antagonist Kemumaki, a Koga Ninja and his ninja cat Kagechiyo. Kemumaki always troubles Kenichi. Kenichi asks Hattori to take revenge as a recurring storyline in many episodes. Although Hattori is a good friend, Kenichi sometimes fights with Hattori due to misunderstandings created by Kemumaki. Sometimes Jippou, Togejirou and Tsubame help him.

Characters

• Kanzo Hattori (ハットリ カンゾウ or 服部 貫蔵 Hattori Kanzō^?)

(voice: Junko Hori, drama actor: Kōtoku Nomura, drama voice: Kazuo Imakura, live-action film actor: Shingo Katori)

A.k.a. Hattori-kun, is the protagonist of the series, a little ninja. He is 11 years old and 40 kg and is 140 centimeters tall. He is the boy who usually contests Kemumaki when he performs mischief. Hattori's main weakness is that he is afraid of frogs and lizards; this often leads him into trouble and becoming helpless around a frog environment. He wears blue coloured ninja robes, with a red belt. He always explains what a good ninja does and what others should also do. His powers can be compared to a master ninja. He also has a strange habit of saying ~degozaru or nin nin after almost every sentence. His girlfriend seems to be Tsubame.

In the Indian (Tamil, Telugu, Hindi and English) versions, Hattori is sometimes his first name and sometimes his last name (along with Shinzo's) it changes between episodes, an inconsistency.

• Shinzō Hattori (ハットリ シンゾウ or 服部 心蔵 Hattori Shinzō^?)

(voice: Yūko Mita, drama actor: Shigeki Nakajō)

A.k.a. Shin-chan, is Kanzo's younger brother. He uses weapons made from wood. He is a ninja-in-training who learns to be a good ninja, like Kanzo. He wears red coloured ninja robes. Shinzo seems to have a good heart and sticks to being loyal to his brother and sometimes gets excited when others are excited. Some of the times, Shinzo tricks Hattori to giving him things. He is also known to cry very loudly, disturbing people and even fainting them. He is also very powerful for his age, at 7 years old. He helps Kanzo fight Kemumaki, with his real weapons and control his loud crying (which immobilizes opponents from attacking) and bites the head of the opponents.

While Kanzo is referred to as "Hattori", Shinzo is usually called by his first name, where his surname is inconsistent in the Indian (Tamil, Telugu, Hindi and English) versions.

• Shishimaru (獅子丸^?)

(voice: Kenichi Ogata)

Is a ninja dog living with Ken'ichi, who came along with Kanzo Hattori and Shinzo Hattori. He is a casual behaving dog who at times becomes lazy and stubborn. Along with Shinzo, the two of them wind up doing mischief and creating trouble. He has an attack of turning in a fireball when provoked. He also has the ability to change form into any other animal. His fur color is yellow. His ninja mark on his forehead is very important for him as it is an identification of him as a ninja. He loves to eat all kinds of delicious treats, especially a fish sausage, or chocolate roll.

• Kenichi Mitsuba (三葉 ケン一 Mitsuba Ken'ichi^?)

(voice: Masako Sugaya, drama actor: Katsumi Takamiya, live-action film actor: Yuri Chinen)

Is a 10-year-old boy who goes to middle school and is poor in his studies. He likes Yumeko, however also Kemumaki is always after her. He also tricks Hattori to help him in any situation, even in extreme ones (e.g. in one episode, he wanted training to become a full-fledged ninja). He also does not follow his mother's instructions properly and often gets a severe scolding from his mother. Though he doesn't study well, he has a good habit of helping others. He is always the victim of Kemumaki's mischievous plans.

• Tsubame (ツバメ^?)

(voice: Fuyumi Shiraishi)

A.k.a. Tsubame-ko, is a kunoichi and classmate of Hattori-kun. She likes Hattori and always wishes to marry him. She has a dislike for Kemumaki and Kagechiyo. She wears pink coloured ninja robes. She seems to own a recorder, a clarinet, a flute, a piccolo and a bassoon, five woodwind instruments.

She is called Sonam in the Hindi version.

• Kemuzo Kemumaki (ケムマキ・ケムゾウ Kemumaki Kemuzō^?)

(voice: Kaneta Kimotsuki, live-action film actor: Gorie)

Is the antagonist of Ninja Hattori-kun. He, along with his cat Kagechiyo (Kemuzo), always are the ones who cause trouble. Strength-wise, he has competition with Hattori and Shinzo. He is 11 years old and is shorter than Kenichi but a lot more fitter and stronger than him. He competes with Kenichi for Yumeko-chan; however when he uses one of his ninja techniques in order to win, Hattori usually steps in to save the day. He wears green colored ninja robes. Only Kagechiyo, Kenichi and the Kanzo family know about his dual life that he's a ninja like Hattori while he joined Kenichi's school as a normal boy in the middle of the series. His parents' whereabouts are unknown, but his mother is noted several times in the series.

He is called Amara in the Hindi dub, but retains his name in the Indian English dub.

• Kagechiyo (影千代^?)

(voice: Eiko Yamada)

Is a talking animal-ninja of the Kōga-ryū, Kagechiyo is the helping antagonist in the series. Usually Kemumaki gives a big task in his plans for Kagechiyo to carry out, which he often does not succeed in. This is because he doesn't get enough training from Kemumaki and is seen sleeping on the streets. He is noticed by Hattori several times. He is seen to have a rivalry with Shishimaru. His fur color is black and white. He normally hides in the Mitsuba house to hear Kenichi and his friends' plans and afterwards informs Kemumaki about them, acting more like a communication device. Sometimes he hates Kemumaki for his strictness and imagines living a life of luxury as a normal cat in some episodes. He enjoys eating fish. He obtains an attack of static electricity on rubbing a shining metal plate against his back. If he uses this attack too much then it will drain his energy, and he will feel weak.

He is called Kiy'yo or Keo in the Indian versions (Hindi, Tamil, Telugu and English).

• Yumeko Kawai (河合 夢子 Kawai Yumeko^?)

(voice: Runa Akiyama)

A.k.a. Yumeko-chan, is the girl who usually causes disputes between Kemumaki Kemuzo and Kenichi Mitsuba. She also attends the same middle school as the two, and she is also the one who causes most of the problems of the plot as both Kemumaki and Kenichi fall in love with her and want to attract Yumeko. Most of the time she appears to be confused. Yumeko seems to be in touch with Hattori sometimes. Yumeko sees Hattori as a big brother and Shinzo as a little brother. She is also seen to like Kenichi. And sometimes people mistake her relationship with Hattori as a romantic one, though in some episodes they are seen to show romance. She is also known to play piano fairly well and hates bell peppers.

• Aiko-Sensei

(voice: Yōko Kawanami)

One of Kenichi's teachers. Koike-sensei has a crush on her. The subject she teaches is unknown. Though in many episodes she is shown teaching the class music.

• Jinchu Hattori

(voice: Tadao Futami)

Hattori-kun and Shinzo's father. He also appear in Perman, when he fights with Perman.

• Jippo

(voice: Junpei Takiguchi, drama voice: Hiroko Maruyama)

A giant turtle monster ninja. He and Hattori are ninja partners.

• Koike-Sensei

(voice: Issei Futamata)

Kenichi's teacher, also appears as a ramen chef in Obake no Q-tarō and sometimes appear as a cameo in Doraemon where he eats ramen. He frequently scolds Kenichi similar to when Nobita is scolded by his teacher in Doraemon. He is caricatured after animator Shin'ichi Suzuki. He also appears in the cartoon "Biriken" and "Ultra B" as Michio's father.

• Kentaru Mitsuba

(voice: Yuzuru Fujimoto, drama actor: Teizō Muta)

Kenichi's father. He usually smokes and comes from his office late in the evening. He likes eating and golf a lot. Though a rather plump man, in some of the episodes, his size seems to change, going from stouter to slimmer.

• Ama Mitsuba

(voice: Nashiwa Yukiko, drama actor: Chiharu Kuri)

The mother of Kenichi. She likes Tsubame and thinks that Kemumaki is a good boy (she has no idea about his dual life). She also appears in an episode of Doraemon, in one of Doraemon's dreams.

• Professor Shinobino

(voice: Reizō Nomoto)

A professor who lives in the United States and invented Togejiro.

• Togejirou

(voice: Hiroko Maruyama)

A cactus having supernatural powers is sent by Professor Shinobino from the United States. Shisimaru does not like Cacto-chan and loves to compete with him.

He is called Cactochan in the English and Hindi version.