intravascular ultrasound (IVUS) and fractional flow reserve (FFR) have both been shown to be superior to angiography in optimizing percutaneous coronary intervention (PCI). However, there is still a lack of comparative studies between PCI optimization using physiology and intravascular imaging head-to-head. The aim of this study was to compare the effectiveness of FFR and IVUS PCI optimization strategies on the functional PCI result (assessed with FFR) immediately post-PCI and at 9-12 months after the treatment of long coronary lesions. This was a single-center study comparing post-PCI FFR between two different PCI optimization strategies (FFR and IVUS). The study included 154 patients who had hemodynamically significant long lesions, necessitating a stent length of 30 mm or more. The procedural outcomes were functional PCI result immediately post-PCI and at 9-12 months after treatment. Clinical outcomes included target vessel failure (TVF) and functional target vessel restenosis rate during follow-up. Baseline clinical characteristics and FFR (0.65 [0.55-0.71]) did not differ significantly between the two groups and the left anterior descending artery was treated in 82% of cases. The FFR optimization strategy resulted in a significantly shorter stented segment (49 mm vs. 63 mm, p = 0.001) compared to the IVUS optimization strategy. Although the rates of optimal functional PCI result (FFR > 0.9) did not significantly differ between the FFR and IVUS optimization strategies, a proportion of patients in the FFR group (12%) experienced poor post-PCI functional outcome with FFR values ≤ 0.8, which was not observed in the IVUS group. At the 9-12 month follow-up, 20% of patients in the FFR group had target-vessel-related myocardial ischemia, compared to 6% in the IVUS group. The rates of TVF and functional target vessel restenosis during follow-up were also numerically higher in the FFR optimization group. The use of FFR PCI optimization strategy in the treatment of long coronary artery lesions is associated with a higher incidence of poor functional PCI result and larger myocardial ischemia burden at follow-up compared to the IVUS optimization strategy. However, this discrepancy did not translate into a statistically significant difference in clinical outcomes. This study highlights the importance of using IVUS to optimize long lesions functional PCI outcomes.