Two core indicators adopted for evaluating tuberculosis (TB) control programmes are treatment outcome and case detection rate (CDR). While the former is easy to report, the CDR can only be estimated (calculated as notifications of new and relapse cases divided by estimated incidence). According to the World Health Organization (WHO), Mozambique has one of the lowest CDRs among the high TB burden countries (HBCs), with 37% in 2013 [1]. In children, calculating CDR is even more challenging, given the difficulty in diagnosing TB and the lack of accurate estimates for paediatric incidence [2]. Several paediatric TB incidence estimates have been published recently [3–5], showing higher figures than those provided by WHO. The large variation in estimates and the lack of population-based data from HBCs (particularly from Sub-Saharan Africa) highlights the urgent need for new data to inform predictive models necessary to implement the “End TB Strategy” and achieve elimination [6]. The objective of this study was to calculate the paediatric CDR in Mozambique and to provide reference methodology and evidence for other countries.