Hematopoietic stem cell transplant (HSCT) is a therapeutic option for patients with sickle cell disease (SCD) and severe acquired aplastic anemia (SAA). HSCT may have beneficial effects on ventricular function in damaged myocardium. We hypothesized improvement in ventricular performance and pulmonary hypertension following HSCT with strain echocardiography in SCD and SAA. Echocardiographic strain and other standard functional data were obtained via retrospective cohort analysis of patients (n = 23) with SCD and SAA who underwent HSCT and were followed at a single center between 2000 and 2014. Left ventricular global longitudinal strain was below normal at baseline, and decreased significantly (from − 16.6 to − 11.1, P = 0.05) from pre-HSCT to the initial post-HSCT echocardiogram at 109 (SD ± 83) days. At 351 (SD ± 115) days, longitudinal strain improved significantly from initial decline (from − 11.1 to − 17.5, P = 0.009) but was comparable to baseline (P = 0.43). Other measurements of bi-ventricular function did not change significantly. Tricuspid regurgitation velocities as surrogates for pulmonary hypertension improved in the subset of patients with baseline elevated values although data points were limited. Abnormal myocardial systolic function was detected at baseline with strain imaging. HSCT was associated with initial worsening longitudinal strain values, followed by improvement to baseline levels by 1 year. Insufficient data exist on whether pulmonary hypertension improves after HSCT.