Lipoprotein-associated phospholipase A2 (Lp-PLA2) is an independent risk factor for plaque rupture and atherothrombotic events. However, the associations between serum Lp-PLA2 level and thrombus burden in ST-segment elevation myocardial infarction (STEMI) patients remain unknown.We consecutively enrolled 351 STEMI patients who underwent primary percutaneous coronary intervention (pPCI). Patients were assigned to a high thrombus burden (HTB) group (n = 230) and a low thrombus burden (LTB) group (n = 121). Baseline data were recorded during hospital admission. Plasma Lp-PLA2 concentration, coronary angiography results, and in-hospital mortality were measured. Plasma Lp-PLA2 level had a high correlation with thrombus burden score (TBS) before pPCI and it was found to be a significant independent predictor of HTB in STEMI patients (P < 0.05). Moreover, TBS, corrected thrombolysis in myocardial infarction (TIMI) frame count (cTFC), and plasma Lp-PLA2 level after pPCI in patients with HTB were significantly higher than those in patients with LTB (P < 0.05). Meanwhile, TIMI flow grade (TFG) and TIMI myocardial perfusion grade (TMPG) of HTB patients were markedly lower than those of LTB patients (P < 0.05). Additionally, correlations of plasma Lp-PLA2 level before pPCI with TFG before pPCI and TBS, cTFC, and TMPG after pPCI were modest (P < 0.05). However, the associations of plasma Lp-PLA2 level after pPCI with TFG, TBS, cTFC and TMPG were low (P < 0.05).These results demonstrated that the plasma Lp-PLA2 level before pPCI is an independent predictor of HTB in STEMI patients, resulting in modestly predicting blood flow and myocardial perfusion of the culprit artery.