In the 1960s, a gifted young medical student tries to make a name for himself. Kuroo Hazama is a reserved young man with unusual black-and-white hair, a body covered with scars, and a dark past. Despite only being a medical student, his surgical brilliance starts to attract attention after he completes a seemingly impossible operation. Together with the spirited and honest intern Maiko Okamoto and Yabu, a close friend with a troubled life, Hazama devotes himself to the world of medicine.

However, his path to becoming a respectable surgeon is a difficult one as student riots, war, and corruption are consuming Japan. Hazama quickly finds himself caught up in a series of nefarious circumstances that challenge his integrity as a person and his path towards becoming a surgeon. Young Black Jack chronicles the story of a man capable of performing unthinkable feats of medicine, and the journey that leads him to become the legend known as Black Jack.