The story of Zombie Loan is basically a modern day mythology that takes place mostly in a city setting, with mystery, suspense, zombies and many secrets to be uncovered.

Two seemingly normal high school boys, Shito and Chika were involved in a deadly bus accident. All the passengers, save for them, died. To make it more mysterious, the two boys apparently survived without a scratch. In truth, they were torn to pieces and the ferryman Bekko put them back together as (legal) zombies. However, he "accidentally" switched their right hands, thus getting them stuck as partners. They must remain close to each other to prevent their respective hands from rotting.

They were given the opportunity to become humans if they paid their zombie loan. In the course of a year they must gather the money to pay their debt, the time limit may be extended, but it would make it a lot more expensive. The fastest way to earn money is by claiming the bounties on illegal zombies, thus Shito and Chika become zombie hunters.

They meet Michiru, a girl from their school who is able to see black rings around people's necks, the mark of death. They realize that they can use her help in tracking hidden illegal zombies, but Michiru is frightened and saddened by her abilities and does not want to be involved.

A near death experience leaves Michiru indebted. She is still a human, but she survived thanks to Bekko slightly altering her fate at the request of Chika and Shito. Thus Shito, Chika and Michiru continue their quest to pay their debts to Z-Loan. Joining them are many other allies and enemies. Some will help them, while others will oppose them seeking power, vengeance, or going after their own goals to challenge fate.