Although letermovir prophylaxis has drastically reduced cytomegalovirus (CMV) infections in allogeneic hematopoietic cell transplantation recipients (allo-HCTR), the broader impact of letermovir prophylaxis remains unclear. We retrospectively analyzed hematological outcomes in CMV-seropositive allo-HCTR (R+) from the pre- and letermovir periods. Among 314 consecutive allo-HCTR+, engraftment was significantly delayed in allo-HCTR+ in the letermovir period, even after removing potential confounders, and despite improved survival. Similar trends were found after reviewing the literature, and this observation should raise vigilance.