Reactivation or reinfection cases of SARS-CoV-2 are known but there is scarce evidence about reactivation in immunocompromised patients. Here, we report the case of a 61-year-old male undergoing a conditioning regimen with fludarabine, cyclophosphamide, and 2-Gy total body irradiation in preparation of a haplo-identical allogeneic hematopoietic stem cell transplantation (allo-HSCT) for acute myeloid leukemia (AML). He received the first dose of a COVID-19 vaccine 6 weeks prior allo-HSCT and was hospitalized a month prior because of a COVID-19 bilateral pneumonia. On discharge, he showed two negative SARS-CoV-2 nasopharyngeal PCR swabs as well as a high SARS-CoV-2 antibody titer. On admission for allo-HSCT, he tested negative for SARS-CoV-2 again. Conditioning with fludarabine, cyclophosphamide, and 2-Gy total body irradiation was started and the patient developed lymphopenia. During his hospital stay, he tested positive for SARS-CoV-2 in a PCR test twice but remained asymptomatic. The conditioning regimen was continued as planned. Later during his stay, the patient showed undetectable SARS-CoV-2 load four times. This case documents possible reactivation of SARS-CoV-2 and raises questions about reactivation risks among recipients of stem cell transplants and other immunocompromised patients.