Infection with Streptococcus pneumoniae is a life-threatening, but vaccine preventable complication in patients with allogeneic hematopoietic stem cell transplantation (allo-HSCT). The international consensus on post allo-HSCT immunization schedules, starting 3–6 months after HSCT, focuses on short-term immunogenicity while long-term immunogenicity is not well characterized. The current Dutch immunization schedule, which starts at 12 months post allo-HSCT, was developed as a result of concerns on the coverage of long-term immunogenicity in international guidelines. We recently encountered two cases of allo-HSCT recipients who developed invasive pneumococcal disease (IPD) despite adequate revaccinations, which led us to question the immunogenicity of pneumococcal vaccinations in this patient group, and whether the currently existing vaccination schedules are appropriate. We included allo-HSCT recipients, vaccinated from one year after transplantation, and tested antibody responses to pneumococcal vaccination. We also performed a systematic review. Antibody concentrations were measured in 42 of 103 (41%) patients, with a response rate of 85% to PCV13 and 62% to PPSV23-unique serotypes. In six relevant studies, protection rates varied between 64 and 98%. Antibody responses in early and late vaccination schedules were similar, but adequate antibody responses were maintained better after late vaccination. Therefore, we propose a vaccination schedule that combines the advantages of early and late vaccination. This new schedule has been introduced since March 2018 in the two academic hospitals in Amsterdam, The Netherlands.