In this study, we aimed to investigate the incidence, risk factors, and clinical outcomes of perianal infections during the pre-engraftment phase after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Consecutive patients who underwent non-T-cell-depleted allo-HSCT at the Peking University Institute of Hematology from January 1 to December 31, 2016 were enrolled (n = 646). Ninety-nine patients were found to have perianal infections during the pre-engraftment phase, and 80 were found to have neutropenia on perianal infection diagnosis. The cumulative incidence of perianal infection during the pre-engraftment phase after allo-HSCT was 15.3%. A history of perianal infection (hazard ratio [HR] = 15.28, p < 0.001) or hemorrhoids before allo-HSCT (HR = 3.09, p = 0.001) was significantly associated with the new occurrence of perianal infection after allo-HSCT. All patients received empirical broad-spectrum antimicrobial therapies, and 97 were cured after treatment. The clinical outcomes at 100 days after allo-HSCT were comparable in patients with and without perianal infections. In summary, patients who had perianal infection or hemorrhoids before allo-HSCT had a higher risk of new occurrence of perianal infection after allo-HSCT. With appropriate treatment, perianal infection during the pre-engraftment phase did not influence the clinical outcomes.