Pulmonary thromboembolism (PTE) is an acute emergency with high mortality and morbidity rates. This study aimed to investigate the importance of Lipocalin-type prostaglandin D synthase (L-PGDS) in predicting mortality and prognosis in PTE. The study prospectively included 90 patients who were admitted to the emergency department and in whom PTE was confirmed by computed tomographic pulmonary angiography as well as 40 healthy volunteers with no disease. L-PGDS levels in the venous blood were measured and compared. Pulmonary embolism severity index (PESI) prognosis scores of all patients and 1-month mortality rate were calculated. There was a statistically significant difference between the L-PGDS levels of the patient and control groups (P = 0.024), and 1-month mortality of patients diagnosed with PTE was 20% (n = 18). Furthermore, the patients were divided into two groups: patients deceased within 1 month following the diagnosis and survivors. L-PGDS levels of the deceased patients were significantly higher than those of the survivors (P < 0.001). Age, systolic blood pressure, pulse, shock index, lactate, and PESI scores were significantly different between the survivors and deceased patients. The cut-off value for L-PGDS obtained using receiver operating characteristic (ROC) curve analysis for 1-month mortality was 815.26 ng/mL (sensitivity: 83.33%; specificity: 79.17%; area under the curve: 0.851; 95% confidence interval 0.760–0.917; P < 0.001). Based on this cut-off value, logistic regression analysis revealed that increased L-PGDS, together with PESI, was an independent indicator of 1-month mortality. L-PGDS is associated with short-term mortality in patients with PTE; therefore, it can be used to predict mortality risk in patients with PTE.