In this study, we aimed to assess levels of serum B cell lymphoma 2 (sBcl-2) in children, which has been implicated in the etiopathogenesis of pulmonary hypertension (PH), as well its association with tissue Doppler echocardiographic imaging (TDI) data and parameters used in the follow-up of PH. The sBcl-2 level was assessed in 35 children with PH (24 had eisenmenger syndrome, and 11 had idiopathic PH) and in 38 healthy children as controls. TDI was performed on 25 patients whose cardiac anatomy allowed the test. The respective sBcl-2 values in patients and controls were 35.69 ± 18.83 and 2.66 ± 7.95 ng/ml (p < 0.001). The sBcl-2 levels were significantly greater in the New York Heart Association (NYHA) functional class 3 patients than those in the NYHA class 2 patients (p = 0.033). The sBcl-2 value in patients who walked <475 m in the 6-min walk distance (6MWD) test was significantly greater than in those who walked ≥475 m (p = 0.038). The sBcl-2 level showed a negative correlation with ejection time measured at the septal anulus (p = 0.026) and a positive correlation with interventricular septum-Tei (p = 0.018). The results of this study showed for the first time that there is an increase in the levels of sBcl-2 as an inflammatory marker and that the sBcl-2 levels are associated with prognostic parameters in children with PH. Because sBcl-2 levels were greater in patients who walked <475 meters during the 6MWD test, we suggest 475 ms as the cut-off value for the 6MWD test to differentiate between a good and a bad prognosis.