Although drug-eluting stents have improved clinical outcomes, percutaneous coronary intervention (PCI) for acute coronary syndrome (ACS) remains a challenging procedure in terms of thrombus management. A new-generation P2Y12 receptor inhibitor, prasugrel, provides more rapid and potent antiplatelet action compared with clopidogrel. Prasugrel achieved significant reduction of ischemic events compared with clopidogrel in ACS. The aim of this optical coherence tomography (OCT) study was to evaluate temporal changes in tissue prolapse after stenting under different antiplatelet regimens (aspirin plus prasugrel or clopidogrel) in ACS patients. A total of 119 ACS patients were randomized to either prasugrel or clopidogrel at the time of PCI. OCT analysis was available in 119 patients at baseline (just after stenting), 77 patients at 2 weeks, and 62 patients at 4 months after stenting. Cross-sectional analysis for every 1 mm was performed at in-stent and adjacent reference segment. Tissue prolapse area was calculated by lumen area minus stent area within the stented segment. Baseline patient and procedural characteristics were not different between the prasugrel and clopidogrel groups. Tissue prolapse area was significantly lower in the prasugrel compared with the clopidogrel group after stenting (0.24 ± 0.23 vs. 0.36 ± 0.23 mm², p = 0.003) and at 2 weeks (0.11 ± 0.13 vs. 0.19 ± 0.16 mm², p = 0.005). However, there was no significant difference at 4 months. In conclusion, our study suggests prasugrel was effective in reducing tissue prolapse in the super acute phase in ACS patients compared with clopidogrel. However, the effect of tissue prolapse reduction was not different up to 4 months follow-up.