To examine the late effects and health-related quality of life among childhood cancer survivors (CCS) after stem cell transplantation (SCT), we performed a cross-sectional survey using self-rating questionnaires. The subjects were divided into 3 groups: SCT-treated CCS, CCS treated without SCT, and the general population who matched for age, gender, residential area, and work status with the CCS. We analyzed the questionnaires of 185 CCS and 1,000 control participants. The median ages of CCS at diagnosis and survey were 8 and 22 years, respectively. The mean final heights of male and female participants were significantly lower for SCT-treated CCS than for CCS treated without SCT and the controls. Among the SCT-treated CCS, >40% were underweight (BMI < 18.5). Late effects were observed in 78% of SCT-treated CCS versus 45% of CCS treated without SCT. Multivariate analysis revealed that >15 years' duration after therapy completion (OR 2.95; p = 0.014), solid tumors (4.31; p = 0.040), radiotherapy (2.82; p = 0.009), recurrence (4.22; p = 0.017), and SCT (3.39; p = 0.014) were significant risk factors for late effects. Subjective symptoms were significantly frequent in SCT-treated CCS. Physical dysfunction, psychological stress, and social adaptation problems were observed in >70% of SCT-treated CCS.