In Brazil, leprosy is endemic and concentrated in high-risk clusters. Internal migration is common in the country and may influence leprosy transmission and hamper control efforts. We performed a cross-sectional study with two separate analyses evaluating factors associated with migration in Brazil's Northeast: one among individuals newly diagnosed with leprosy and the other among a clinically unapparent population with no symptoms of leprosy for comparison. We included 394 individuals newly diagnosed with leprosy and 391 from the clinically unapparent population. Of those with leprosy, 258 (65.5%) were birth migrants, 105 (26.6%) were past five-year migrants, and 43 (10.9%) were circular migrants. In multivariate logistic regression, three independent factors were found to be significantly associated with migration among those with leprosy: (1) alcohol consumption, (2) separation from family/friends, and (3) difficulty reaching the healthcare facility. Separation from family/friends was also associated with migration in the clinically unapparent population. The health sector may consider adapting services to meet the needs of migrating populations. Future research is needed to explore risks associated with leprosy susceptibility from life stressors, such as separation from family and friends, access to healthcare facilities, and alcohol consumption to establish causal relationships.