Congenital neutropenia (CoN) is a heterogeneous group of inborn errors of immunity (IEI) characterized by recurrent infections and early onset of neutropenia (NP). This study aimed to investigate the demographic and clinical data of children with CoN and idiopathic neutropenia (IN) in Morocco. We performed a retrospective study of patients with CoN and analyzed the clinical and laboratory findings of patients with CoN and IN diagnosed between 1999 and 2018 in a clinical immunology unit of a large pediatric hospital. We identified 88 patients, 51 with IN and 37 with CoN. Fifty-seven percent were males, and 43% were females, ranging from 1 month to 19 years. The median age at onset was 8 months, and the median at diagnosis was 36 months. Consanguinity was observed in 57% of the cases, and a history of recurrent infections in the siblings was found in 27.3%. The most common infectious complications were ear, nose, and throat (ENT) infections, skin and soft tissue infections, and lung infections. Patients with CoN were classified into seven syndromes: 9 with severe congenital neutropenia, 11 with cyclic neutropenia, 6 with glycogen storage disease type 1b, 5 with poikiloderma with neutropenia, 3 with Griscelli syndrome, 2 with Hermansky-Pudlak syndrome type II, and 1 with Cohen syndrome. This study provides a comprehensive overview of CoN and IN in a pediatric cohort from Morocco, representing the country's most considerable single-center investigation of these conditions. Our findings highlight the significant burden of CoN, accounting for 5% of IEI in the Moroccan registry, a proportion higher than in some neighboring countries. The study emphasizes the early onset and severity of bacterial infections in CoN patients, underlining the critical need for timely and accurate diagnosis.