Abstract Background Pneumocystis jirovecii pneumonia is an opportunistic infection that most frequently affects immunocompromised people, especially patients with HIV; clinical presentation is nonspecific and mortality rate in patients without HIV ranges are between 30% and 75%. In the international literature, there are few case reports of pediatric oncology patients. A series of cases is presented with the objective of describing the epidemiological characteristics, clinical presentation, treatment, and outcomes of Pneumocystis jirovecii pneumonia in this population group. Methods An observational, descriptive, and retrospective study was carried out in cancer patients under 18 years, with clinically compatible symptoms, an imaging study suggestive of the pneumonia, and identification of P. jirovecii using a PCR test of bronchial aspirate at Hospital Infantil Teletón de Oncología in Querétaro Mexico, since November 2014 to June 2023. Results A total of 17 events were reported with a median age of 9.8 years, 14/17 (82%) with a diagnosis of acute leukemias, 1/17 (6%) Ewing sarcoma, 1/17 (6%) lymphoma large cell anaplastic and 1/17 (6%) neuroblastoma. Regarding their therapeutic phases, 7/17 (41%) were in consolidation, 4/17 (23%) induction, 3/17 (18%) allogeneic HSCT (Hematopoietic stem-cell transplantation), 2/17 (12%) in surveillance, and 1/17 (6%) in maintenance. The clinical presentation in our patients was characterized by the presence of fever in 15/17 (88%), dry cough in 10/17 (59%) and 17/17 (100%) developed acute respiratory distress syndrome, which was classified as mild in 7/17 (41%), moderate in 5/17 (29%) and severe in 5/17 (29%). 13/17 (75%) presented distributive shock. All our patients underwent chest x-rays, 12/17 (70.5%) presented bilateral interstitial infiltrate, 4/17 (23.5%) consolidation, and 1/17 (6%) pleural effusion. Lung CT (computed tomography) was performed in 4/17 (23.5%), and 4/4 (100%) presented ground glass opacities. All of our patients were admitted to the PICU (Pediatric intensive care unit) and 16/17 (94%) required invasive mechanical ventilation. All receive treatment with TMP-SMX (Trimethoprim-sulfamethoxazole). 4/17 patients died (23%) of whom none received prophylaxis. 3/17 patients (18%) received prophylaxis with trimethoprim-sulfamethoxazole (TMP-SMX). Conclusion The present study is the first study in Mexico that compiles cases of Pneumocystis Jirovecii pneumonia in pediatric oncology patients. P. jirovecii pneumonia remains a rare cause, but represents a potentially fatal cause in oncology patients, so it is important to have a high clinical suspicion during the evaluation of an immunocompromised patient with evidence of pneumonia during all treatment phases with chemotherapy, in order to start treatment promptly. Thus, we also emphasize the importance of adequate prophylaxis as the most important preventive measure.