Right ventricular dysfunction (RVD) defined by echocardiography and/or by natriuretic peptides is a well-known predictor of prognosis in patients with pulmonary embolism (PE). This study investigated carbonic anhydrase IX (CA IX) levels for predicting echocardiographic RVD in patients with PE. A total of 150 normotensive patients with PE were included. The levels of CA IX, N-terminal pro-brain-type natriuretic peptide (NT-proBNP), and high-sensitive cardiac troponin T were significantly elevated in patients with PE with RVD on echocardiography. A receiver–operating characteristic curve analysis showed a value of 0.751 for CA IX, 0.714 for NT-proBNP, and 0.650 for high-sensitive troponin-T to predict RVD on echocardiography. The cutoff value to predict RVD was 32.45 pg/mL for CA IX (sensitivity: 89.3% and specificity: 51.1%). There was a significant positive correlation between the CA IX level and the systolic pulmonary arterial pressure on echocardiography ( = .21; P = .035). The CA IX is a significant serologic predictor of RVD in acute PE and correlates with systolic pulmonary arterial pressure.