Hematopoietic stem cell transplantation (HSCT) is a curable therapy for paediatric cancer. Cardiovascular complications are the leading cause of late morbidity and mortality in long-term childhood cancer survivors. However, cardiac function in children after HSCT is not well known. We assessed left-ventricular (LV) function in children after HSCT for acute leukaemia by using tissue Doppler imaging (TDI) and speckle tracking echocardiography (STE). Forty consecutive patients (median 11.9 years) who had HSCT for acute leukaemia between 2011 and 2014 had undergone an echocardiographic assessment before and after (median 9.2 month) HSCT. LV function parameters, including conventional, TDI, and STE data, were collected from patients’ echocardiographic data, and were compared with those of controls (n = 39, median age 9 years). All patients had anthracycline as a pre-HSCT chemotherapy. At post-HSCT, patients had decreased LV ejection fraction (p = 0.06), rate-corrected velocity of fibre shortening (p = 0.04), and mitral septal annular E’ velocity (p = 0.03) compared with controls. STE parameters also decreased in patients; mid LV global circumferential strain (p < 0.01), and mid LV global circumferential systolic strain rate (SR, p = 0.01). There was no significant change in LV function parameters after HSCT compared with pre-HSCT study. Patients with anthracycline cumulative dose > 400 mg/m² showed significantly lower mid LV global circumferential strain (p < 0.05) and mid LV global circumferential diastolic SR (p < 0.05). Patients who received HSCT for acute leukaemia had subclinical cardiac dysfunction, which may be associated with pre-HSCT anthracycline exposure with little effect of conditioning regimens. Serial monitoring of cardiac function is mandatory in all children following HSCT.