Abstract Objective There is a relative lack of information about infections occurring in children following allogeneic hematopoietic stem cell transplants (allo‐HSCT) in developing countries. Herein, we describe the incidence rates of different infections according to the transplant period and baseline condition in Colombia. Methods In a retrospective cohort study of all children who underwent allo‐HSCTs from 2012 to 2017 in a hospital in Cali, Colombia, we reviewed medical records from the first post‐transplant day until day + 365 to describe microbiologically confirmed incidence rates of infections and deaths during three post‐transplant periods and according to baseline condition. Results Most allo‐HSCT (n = 144, 96%) were followed by infections over the following year, mostly due to bacteria and cytomegalovirus (4.3 and 3.3 per 1000 patient‐days, respectively). Children were at the highest risk for infection in the first 30 days post‐HSTC, but mortality was highest after 100 days. Overall, high mortality (n = 44, 31.7%) was associated with infections, especially from extensively drug‐resistant bacteria, adenovirus, and aspergillosis. Infection rates were similar independent of the baseline condition. Conclusion Almost all children in this cohort developed infections post allo‐HSCT. Describing the distribution of infections throughout the first post allo‐HSCT year allows clinicians to narrow the differential diagnosis of infections according to the post‐transplant period. This is especially useful when prioritizing interventions in children receiving HSCT in stringent healthcare systems in developing countries.