Very late stent thrombosis (VLST) is a rare but serious complication following percutaneous coronary intervention (PCI). S100A8/A9 plays an important role in thrombosis through modulating the inflammatory response. This observational study aimed to reveal the association between S100A8/A9 and VLST. Continuous blood samples were collected from patients at both the time of index PCI for acute myocardial infarction (AMI) and the time of PCI for VLST (VLST group) or follow-up coronary angiography (AMI group). In all, 56 patients were selected in each group from a cohort of 8476 patients and other 112 individuals who underwent health checkups (normal control [NC] group) were selected as controls. Serum levels of S100A8/A9 and high sensitivity C-reactive protein (hs-CRP) were tested and compared. The mean level of S100A8/A9 was 3754.4 ± 1688.9 ng/mL during index PCI and increased to 5517.8 ± 2650.9 ng/mL at the time of VLST; in the AMI group, S100A8/A9 level was 2434.9 ± 1243.4 ng/mL during index PCI and decreased to 1568.2 ± 772.1 ng/mL during follow-up, similar to that detected in the NC group (1618.2 ± 641.4 ng/mL). Of note, S100A8/A9 levels showed significant increases during VLST when compared to its own levels during index PCI, which was different from the changes of hs-CRP. Higher serum levels of S100A8/A9 are associated with the development of VLST.