Atypical teratoid/rhabdoid tumor (AT/RT) of the central nervous system (CNS) is an aggressive malignant tumor that is mainly found in younger children and is associated with poor prognosis. Our objectives: to present the results of treatment of children with CNS AT/RT under 3 years of age and assess the impact of various prognostic factors on patient survival. The study was approved by the Independent Ethics Committee and the Scientific Council of the N.I. Pirogov Russian National Research Medical University of Ministry of Healthcare of the Russian Federation. The study included 106 patients with CNS AT/RT aged 0–3 years who had been treated and monitored from 2008 to 2020. The median age was 16 (9; 23) months. All the patients underwent primary tumor resection with subsequent chemotherapy according to various protocols. At the time of the analysis, 47 patients (44.4%) were alive, 1 patient (0.9%) was lost to follow-up and 58 patients (54.7%) were dead, of whom 52 patients (90%) had died of disease progression and 6 (10%) – of polychemotherapy complications. One patient developed shunt-related intra-abdominal metastasis within 10 months of the diagnosis. The 1-year progression-free survival (PFS) was 0.50; the 2-year PFS was 0.29; the 5-year PFS – 0.27. The median PFS was 12 months. The 1-year overall survival (OS) was 0.72; the 2-year OS was 0.53; the 5-year OS – 0.40. The median OS was 27 months. An analysis of patients with CNS AT/RT under 3 years of age showed that PFS was statistically significantly higher in: children aged > 12 months; children with totally resected tumours; children who had received polychemotherapy in accordance with the ATRT-2006 protocol that included radiotherapy and regional administration of a triplet of chemotherapeutic agents. The OS in patients with CNS AT/RT aged < 3 years was statistically significantly higher in: children aged > 12 months; children who had been treated with radiation therapy; patients who had received cytosar/etoposide intrathecally/intraventricularly; patients who had undergone high-dose chemotherapy with subsequent autologous hematopoietic stem cell transplantation. A multivariate analysis revealed that PFS was influenced by age, tumor location, extent of resection and exposure to radiation therapy, regional chemotherapy or high-dose chemotherapy with autologous hematopoietic stem cell transplantation, while OS was affected by age and exposure to radiation therapy.