We retrospectively analyzed 60 cases of pediatric patients who received allogeneic stem cell transplantation (SCT) between 2000 and 2008, using the tentative scoring system for evaluation of early (<30 days) coagulation disorders. In the 41 patients who survived, D-dimer levels showed a transient increase 2 weeks after SCT and normalized thereafter, but these levels were persistently elevated in the 19 patients who died. Of 19 patients with a positive score, 11 died of transplantation-related complications [transplantation-related mortality (TRM) = 0.579] within 1 year, while none of the 41 with a negative score died during the same period. Since 2009, 12 of 30 patients had positive scores within 30 days after SCT. Intervention with recombinant human thrombomodulin (rhTM) was introduced for patients with a positive score, and 10 of these patients survived (TRM = 0.167) along with a dramatic improvement of D-dimer level. Although the effects of this treatment were observed in a limited number of patients, our observations suggest that early coagulation disorder after allogeneic SCT is a strong prognostic factor for TRM, and that intervention with rhTM improves TRM.