Hematopoietic stem cell transplantation (HSCT) is now widely practiced worldwide. It has the potential to cure many hematological diseases, such as acute leukemia and thalassemia. As an emerging country, Malaysia has made advancements despite many challenges. HSCT has evolved rapidly since the first pediatric allogeneic HSCT case in 1987. The first adult HSCT was performed 5 years later in 1993. Currently, a total of 13 hospitals offer HSCT services throughout Malaysia. These include private healthcare services, substantially funded government hospitals governed by the Ministry of Health, and partially funded teaching hospitals governed by the Ministry of Education. Until 2015, 1,987 allogeneic and 1,648 autologous HSCT procedures were performed. This article narrates the history and development of HSCT in Malaysia and briefly discusses the challenging issues in this area.