Abstract Background Given the limited specificity of D-dimer, there is a perceived need to discover a more precise marker for diagnosing individuals who are suspected of having pulmonary embolism (PE). In this study, by evaluating the increase in the serum level of Apelin-13 and D-dimer, we found valuable findings about Apelin-13, which can be suggested as an auxiliary and non-invasive diagnostic biomarker in individuals with suspected PE, based on the obtained results. Methods In this case-control study, 52 Iranian individuals were included, all of whom were suspected to have PE. These individuals were then divided into two groups based on the results of CT angiography, which is considered the gold standard imaging method for diagnosing PE. The two groups were patients with PE and patients without PE. Finally, the levels of certain markers in the serum were compared between the two groups. Results The mean serum D-dimer levels in patients with PE were significantly elevated (p