Infectious diseases play a critical role in determining the profitability of individual farms and maintaining the viability of livestock industries, international trade, and trade policies. Thus, it is critical to analyze the economic consequences of infectious diseases, and the effects of producer strategies to control or eliminate diseases in a cost efficient approach. Also, important is the goal to rally support for the development of public disease control programs. This study examined the long-term feasibility and effectiveness of various producer strategies to prevent and control Johne’s disease in dairy herds, an infectious and incurable disease which has significant economic repercussions for the dairy industry. There are few previous studies available on the economic aspects of Johne’s disease and there remains a knowledge gap with regard to the economics of the disease and the economic justification of the disease controls associated with the biological characteristics of the disease. This study contributes to this body of knowledge. We constructed an optimal control model integrating the biology of animals and disease into an economic framework to estimate the best control method in terms of maximizing an individual farm’s profit and minimizing disease elimination periods. Our results show that any Johne’s disease control method yields a higher net present value compared to no control. Implementing a single control strategy can control the disease, but a combination of control strategies in different categories is the most profitable and effective way to reduce the infection rate in a disease-infected herd. The results of the study are directly applicable to managing this disease on US dairy farms and contribute to controlling a high-priority pathogen in an important industry.