In light of the various adverse effects of Johne's disease on animal productivity and the debate on the role of its causative organism, Mycobacterium avium ssp. paratuberculosis, in the etiology of Crohn's disease, major dairy-producing countries around the world have implemented national control programs aimed at reducing the prevalence of this infection in cattle. A pilot control program was initiated in Ireland in 2013, with a key objective to provide farmers with test-negative dairy herds with tools and knowledge to increase their confidence of freedom over time. The aim of this study was to estimate the confidence of freedom obtained in test-negative Irish dairy herds over time with various sampling scenarios and to evaluate the cost-effectiveness of alternative scenarios for achieving an acceptable level of confidence of freedom in herds with no evidence of infection. A stochastic model was developed to simulate repeated annual testing of individual animals using ELISA and confirmatory assays over a period of 20 yr. Two scenarios modeled the current herd-screening options, whereas 14 alternative scenarios explored the effect of varying parameters from the current testing strategies, such as the frequency of testing, the eligibility criteria for selecting animals, the type of assay, the probability of introduction, and the assay sensitivity. Results showed that the current testing strategy with milk twice a year or serum once a year in all animals over 2 yr old provided the highest annual herd sensitivity, with a median value of 55%. Although the median confidence of freedom increased over time for all scenarios, the time required to reach 90 and 95% confidence of freedom was highly variable between scenarios. Under the testing scenario where serum tests were used once a year, the confidence of freedom reached 90% after 4 yr and 95% after 7 yr of testing. Some of the alternative scenarios achieved an acceptable level of confidence of freedom in a reasonable timeframe and at lesser cost than the current testing strategies. The results of this work are used to provide recommendations for the next phases of the program.