The optimal timing of pretreatment with prasugrel in percutaneous coronary intervention (PCI) for acute coronary syndrome (ACS) is unclear. We used optical coherence tomography (OCT) to compare in-stent thrombus volume immediately after PCI between the administration of low-dose prasugrel (20 mg loading dose) at the time of diagnosis of ACS (early prasugrel: n = 34) and the administration of low-dose prasugrel immediately after diagnostic angiography prior to PCI for ACS (late prasugrel: n = 56). The durations between the administration of prasugrel and OCT in the early prasugrel group and late prasugrel group were 5.1 ± 6.5 and 0.9 ± 0.7 h, respectively (p < 0.001). OCT detected thrombus/plaque protrusion in all stented segments. In-stent thrombus/plaque protrusion volume (2.92 ± 1.96 vs. 6.48 ± 4.97 mm³, p < 0.001), mean in-stent thrombus/plaque protrusion area (0.13 ± 0.07 vs. 0.29 ± 0.23 mm², p < 0.001) and maximum in-stent thrombus/plaque protrusion area (0.70 ± 0.36 vs. 1.06 ± 0.56 mm², p < 0.001) were significantly smaller in the early prasugrel group as compared with the late prasugrel group. The administration of prasugrel at the time of diagnosis of ACS was associated with significantly reduced in-stent thrombus/plaque protrusion immediately after PCI as compared with the administration of prasugrel after the coronary angiography prior to PCI.