Objectives Leprosy is a chronic infectious disease caused by Mycobacterium leprae. The PEP4LEP project will compare two integrated skin-screening interventions combined with the distribution of a single dose of rifampicin as post exposure prophylaxis (SDR-PEP) for contacts of leprosy patients. To implement the study in Mozambique, it was necessary to assess recent epidemiological indicators of leprosy and to estimate case detection delay as a main outcome indicator at baseline. Methods This was a descriptive study to establish the trend of epidemiological indicators of leprosy in the Nampula province districts Murrupula, Meconta and Mogovolas in Mozambique, between 2015 and 2019; and to calculate the average delay to diagnose leprosy cases in these districts. The National Leprosy Control Programme was also described. For the estimation of the case detection delay, 81 recently diagnosed patients were interviewed. Results There were 939 new leprosy cases detected in the three districts from 2015 to 2019, with a high proportion of disability (17.0%). The mean diagnosis delay was 26.6 months (95% CI: 18.4–34.7), while the median was 17.0 months. Multibacillary cases had an average delay of 27.9 months (95% CI: 18.6–37.1), while those with grade 2 disability had an average delay of 47.8 months (95% CI: 15.4–80.2). Conclusion The long case detection delay and high grade 2 disability rates indicate that there is a need for active case finding and chemoprophylaxis with SDR-PEP to help interrupt the chain of Mycobacterium leprae transmission in Nampula province.