Risks associated with isolated great saphenous vein (GSV) thrombosis remain controversial. The purpose of this study is to identify the risk of pulmonary embolism (PE) in patients with isolated GSV thrombosis, particularly those with thrombus within 3 cm of the sapheno-femoral junction. A retrospective chart review of color flow Doppler lower extremity venous ultrasound examinations from an academic hospital from 2011 to 2016 was conducted. Seventy-eight patients were identified as having acute thrombus in their GSV and were then further stratified based on the presence or absence of concomitant deep venous thrombosis (DVT). A control group of 49 patients who presented with leg swelling and were found to have a normal color flow Doppler examination was also identified. Patients without thrombus (n = 49), patients with isolated GSV thrombus (n = 29), and patients with GSV thrombus with concomitant DVT (n = 49) underwent full chart review to determine whether any patients developed PE. This was diagnosed specifically by computed tomography angiogram or ventilation/perfusion scan, within 60 days of initial diagnosis of lower extremity thrombus. In our analysis, there was no significant difference in the risk of PE in patients with isolated GSV thrombus compared with a control group of normal patients (3.5% vs 2.0%, P = 0.38). However, patients with GSV thrombus and concomitant DVT had a significantly increased risk of PE compared with patients with isolated GSV thrombus (26.5% vs 3.5%, P = 0.01). We found that the risk of PE in patients with isolated GSV thrombus is not significantly increased compared with a normal cohort.