Recent studies have reported that a novel cardiac biomarker, heart-type fatty acid-binding protein (h-FABP), significantly predicts mortality inpatients with pulmonary embolism (PE) at intermediate risk. The aim of this study was to evaluate the effect of thrombolytic therapy on prognosis of the intermediate risk acute PE patients with elevated levels of h-FABP. This is non-interventional, prospective, and single-center cohort study where 80 patients (mean age 62 ± 17 years, 32 men) with confirmed acute PE were included. Only patients with PE at intermediate risk (echocardiographic signs of right ventricular overload but without evidence for hypotension or shock) were included in the study. h-FABP and other biomarkers were measured upon admission to the emergency department. Thrombolytic (Thrl) therapy was administered at the physician's discretion. Of the included 80 patients, 24 were h-FABP positive (30%). 14 patients (58%) with positive h-FABP had clinical deterioration during the hospital course and required inotropic support and 12 of these patients died. However, of 56 patients with negative test, only 7 patients worsened or needed inotropic support and five patients died during the hospital stay. Mortality of patients with PE at intermediate risk was 21%. The 30-day mortality rate was significantly higher in h-FABP(+) patients compared to h-FABP(-) patients (9 vs. 50%, p < 0.001). Multivariate analysis revealed h-FABP as the only 30 day mortality predictor (HR 7.81, CI 1.59-38.34, p = 0.01). However, thrl therapy did dot affect the survival of these high-risk patients. Despite, h-FABP was successful to predict 30-days mortality in patients with PE at intermediate risk; it is suggested to be failed in determining the patients who will benefit from thrl therapy.