Treatment of non-Hodgkin lymphomas (NHL) in children using risk-based chemotherapy protocols is currently effective in 80–95% of cases, even in advanced stages of the disease. However, relapsed/refractory forms of NHL (which are less common) have an extremely unfavorable course with low survival rates. The addition of autologous and allogeneic hematopoietic stem cell transplantation (HSCT) to a comprehensive treatment program for relapsed/refractory forms of NHL can improve treatment results due to the antitumor effect of chemotherapy drugs of the conditioning regimen and the graft-versus-tumor effect, which is, however, less significant than in leukemia. Moreover, post-transplant complications after allogeneic HSCT in some cases can offset its positive results in NHL; therefore, to reduce toxicity, especially in severe somatic status of the patient, preference is often given to reduced-intensity conditioning regimens. This article presents two clinical cases. In one case, autologous HSCT was carried out for the first relapse of Burkitt's lymphoma. However, the patient developed a second relapse and underwent allogeneic HSCT from a haploidentical donor. In the second case, HSCT from an unrelated HLA identical donor was carried out in a patient with relapsed anaplastic large cell lymphoma. Both patients received reduced-intensity conditioning regimens. This approach helped to avoid the development of severe post-transplant complications, ensuring successful engraftment and achievement of donor hematopoietic chimerism. Early after transplantation, the patient with relapsed Burkitt's lymphoma developed a second tumor – acute T-lymphoblastic leukemia, from which the patient died. Despite treatment with targeted drug crizotinib, the second patient showed lymphoma progression, which resulted in death. The patients' parents gave consent to the use of their children's data, including photographs, for research purposes and in publications.