Previous studies have demonstrated the higher accuracy of frequency-domain optical coherence tomography (FD-OCT) for quantitative measurements in comparison with intravascular ultrasound (IVUS). However, those analyses were based on the cross-sectional images. The aim of this study was to assess the accuracy of FD-OCT for longitudinal geometric measurements of coronary arteries in comparison with IVUS. Between October 2011 and March 2012, we performed prospective FD-OCT and IVUS examinations in consecutive 77 patients who underwent percutaneous coronary intervention with single stent. Regression analysis and Bland–Altman analysis revealed an excellent correlation between the FD-OCT-measured stent lengths and IVUS-measured stent lengths (r = 0.986, p < 0.001; mean difference = −0.51 mm). There was an excellent agreement between the actual stent lengths and the FD-OCT-measured stent lengths (r = 0.993, p < 0.001) as well as between the actual stent lengths and the IVUS-measured stent lengths (r = 0.981, p < 0.001). The difference between the actual stent lengths and the FD-OCT-measured stent lengths was significantly smaller than that between the actual stent lengths and the IVUS-measured stent lengths (0.15 ± 0.68 vs. 0.70 ± 1.15 mm, p < 0.001). Both FD-OCT (mean difference = −0.04 and −0.04 mm, respectively) and IVUS (mean difference = −0.06 and −0.06 mm, respectively) showed an excellent intra-observer and inter-observer reproducibility for the stent length measurements. In conclusion, FD-OCT provides accurate longitudinal measurement with excellent intra-observer and inter-observer reproducibility. FD-OCT might be a reliable technique for longitudinal geometric measurement in human coronary arteries.