Backgroud and Objectives Right ventricular (RV) dysfunction and some biochemical markers were used in the risk stratification of acute pulmonary thromboembolism (PTE). The aim of this study was to investigate the relation between computed tomographic angiographic (CTA) evidence of RV dysfunction and risk-related biochemical markers in patients with acute PTE. Methods A total of 82 patients with acute PTE were divided into two groups by CTA evidence of RV dysfunction; the patients with RV dysfunction (group I, n=49, 63.0짹15.2 years, 32 females) versus the patients without RV dysfunction (group II, n=33, 65.8짹14.0 years, 19 females). Biochemical markers such as N-terminal pro B type natriuretic peptide (NT-proBNP), cardiac enzymes, high sensitivity C-reactive protein (hsCRP), and D-dimer were measured and analyzed between the groups. Results The levels of biochemical markers were as follows; 3922.22짹4192.86 pg/ml in NT-proBNP, 0.09짹0.21 ng/mL in cardiac-specific troponin T (cTnt), 0.68짹2.17 ng/mL in cardiac-specific troponin I (cTni), 119.91짹131.20 U/L in creatine kinase (CK), 8.65짹8.34 U/L in MB fraction of CK, 4.15짹5.20 mg/dL in hsCRP, and 1.61짹2.29 mg/L in D-dimer. The level of NT-proBNP was significantly higher in group I than in group II (5334.72짹6867.46 vs 1685.19짹4144.02 pg/mL, p= 0.015). However, the other biochemical markers were not different between the groups. By receiver operation curve analysis, the optimal cut-off value of NT-proBNP to predict CTA based RV dysfunction was 731.75 pg/mL (sensitivity: 80.6%, specificity: 76.2%). Conclusion The results of this study demonstrated that NT-proBNP is a strong biochemical predictor of RV dysfunction by CTA. NT-proBNP may be used as a simple and available biochemical marker in the risk stratification of acute PTE.