日本室町时代中叶,当权的幕府威信锐减。野心勃勃的醍醐景光(中井贵一饰),为了成就霸业,而将尚未出生的儿子百鬼丸献祭给48个魔神,他和妖怪定下约定,取走了包括眼、耳、口、鼻等在内的48个器官。 一出生就缺少器官部位的百鬼丸,被抛入河中,后来为医生养父(原田芳雄饰)所救,替他制作了义眼、义肢等补足了身上缺失,并命名为百鬼丸(妻夫木聪饰),抚养他长大。为了摆脱自己被诅咒的命运,夺回身体的每一个部分,百鬼丸向占有自己器官的48个魔神宣战,离家踏上征战之旅。 在寻找魔神的旅途上,百鬼丸遇到了自称“侠盗”的多罗罗(柴崎幸饰),为了得到百鬼丸手中的宝剑,多罗罗跟随他一起踏上旅程。In the year 3048, the wounded Lord Kagemitsu Daigo proposes a deal to rule the whole world to forty-eight demons in their sealed temple. In return, the demons ask forty-eight parts of the body of his unborn son. When the mutilated baby is born, his mother puts him in a basket in the river flow to save his life. The baby survives and becomes the demon slayer Hyakkimaru that slash demons to retrieve his body parts. During his journey, he meets the female thief Dororo, who was raised as a boy after the death of her parents by the evil Lord Daigo, in a small town and she befriends Hyakkimaru and joins him in his quest seeking revenge against the Daigo's clan.