Despite improved diagnostic tests, extensive education programs, demonstration of the infection's significant costs, and continued investigation of M. paratuberculosis' potential as a food-borne zoonotic agent, paratuberculosis control programs are not being widely adopted by dairy producers. Possible reasons include a failure of experts to justify the economics of control programs, to appreciate how costly control programs are to producers, and an inflexibility in program design that does not incorporate differing dairy size, infection prevalence, productivity, or milk prices. A previous economic test-and-cull decision analysis model was strengthened and updated with current epidemiologic information. Created using Excel® and PrecisionTree® software, the model incorporates costs and benefits of herd management changes, diagnostic testing, and different management actions based on test results to control paratuberculosis in commercial dairy herds. This novel “JD-tree” model includes a herd management decision node (4 options), a test/no test decision node (2 options), a diagnostic test choice decision node (5 options), test result chance nodes (4 levels of possible results), and test action decision nodes (3 options; cull, manage, no action). The model culminates in a chance node for true infection status. Outcomes are measured as a net cost-benefit value to the producer. The model herds demonstrate that herd management to control infection spread (hygiene) is often more economical than testing; not all herds should test as part of a paratuberculosis control program. For many herds, low-cost tests are more useful than higher cost, more sensitive tests. The model also indicates that test-positive cows in early stages of infection may be retained in the herd to generate farm income, provided they are managed properly to limit infection transmission. JD-tree is a useful instructional tool for veterinarians wanting to understand the complex interactions affecting the economics of paratuberculosis control and for defining the specifications of better diagnostic tests