Mucormycosis is a life-threatening infection which causes unacceptably high morbidity and mortality despite treatment. Therefore, a vaccine to prevent mucormycosis is desirable. A major barrier to developing an anti-mucormycosis vaccine is the perception that such a vaccine would not be cost-effective to deploy because the disease is rare. We used data from a recent retrospective study to calculate the annual cost to the US healthcare system caused by mucormycosis infections. We created a model to estimate the cost-efficacy of a niche, anti-mucormycosis vaccine deployed in a targeted manner to high-risk patients. We found that each case of mucormycosis results in an average direct cost to the US healthcare system of $97,743, for an overall cost of mucormycosis of $50 million per year. In the base case scenario, targeted deployment of an anti-mucormycosis vaccine would result in a net cost per quality adjusted life year saved (QUALY) of $17,249. Variations in the price of the vaccine, its market penetration, or the cost of infection could dramatically decrease the net cost, and could even result in net savings per QUALY. In conclusion, mucormycosis causes considerable cost to the US health care system. Targeted deployment of a niche vaccine could decrease infection rates and mortality from mucormycosis in a cost-effective manner.