Background: Our study objectives were to evaluate the medical economics of cervical cancer prevention and thereby contribute to cancer care policy decisions in Japan. Methods: Model creation: we created presence-absence models for prevention by designating human papillomavirus (HPV) vaccination for primary prevention of cervical cancer. Cost classification and cost estimates: we divided the costs of cancer care into seven categories (prevention, mass-screening, curative treatment, palliative care, indirect, non-medical, and psychosocial cost) and estimated costs for each model. Cost-benefit analyses: we performed cost-benefit analyses for Japan as a whole. Results: HPV vaccination was estimated to cost $291.5 million, cervical cancer screening $76.0 million and curative treatment $12.0 million. The loss due to death was $251.0 million and the net benefit was -$128.5 million (negative). Conclusion: Cervical cancer prevention was not found to be cost-effective in Japan. While few cost-benefit analyses have been reported in the field of cancer care, these would be essential for Japanese policy determination.