What is known and objective Patients who receive hematopoietic stem cell transplantation (HSCT) are usually administered a calcineurin inhibitor. Because vancomycin is associated with an increased incidence of nephrotoxicity, neutropenic patients receiving HSCT are considered a high-risk population for nephrotoxicity with vancomycin. We retrospectively compared the efficacy and safety of vancomycin and teicoplanin in febrile neutropenic patients receiving HSCT. Methods A single-centre, retrospective cohort study was conducted at the 614-bed Gifu University Hospital in Japan. Patients who received HSCT and were administered vancomycin or teicoplanin by injection for febrile neutropenia from 1 January 2012 to 31 August 2017 were enrolled. Time to attain an effective trough concentration, clinical efficacy and adverse events were compared between the two groups. Results Time to attain an effective trough concentration of over 10 mu g/mL tended to be shorter in the teicoplanin group than in the vancomycin group (median 3, 95% confidence interval [CI] 2.4-3.6 days vs median 6, 95% CI 1.5-10.5 days; hazard ratio [HR] 0.4, 95% CI 0.15-1.06; P = .066). The rate of clinical failure was lower in the teicoplanin group than in the vancomycin group (18.8% vs 53.8%, P = .113). In addition, the overall incidence of nephrotoxicity was significantly lower in the teicoplanin group (0% vs 46.2%, P = .004). What is new and conclusion Our findings suggest that administration of teicoplanin may lead to early attainment of the effective concentration with a lower rate of clinical failure and incidence of nephrotoxicity compared to vancomycin in febrile neutropenic patients receiving HSCT.