Stent invagination (SIV) sometimes occurs during interwoven nitinol stent (IWS) placement due to its complex deployment system. It may cause stent malapposition and reduce the minimum stent area. However, the clinical implications of SIV remain unclear. This retrospective single-center study sought to assess the clinical implications of IWS invagination in the femoropopliteal lesions in patients with peripheral arterial diseases. Thirty-two consecutive patients (23 men, mean age of 74 years, 34 limbs) with symptomatic femoropopliteal lesions who had received IWS implantation from January to July 2019 were enrolled. The study was approved by the ethics committee of our institution. The 12-month primary patency rate after the initial IWS placement was evaluated as the primary outcome, which was compared between lesions with SIV (SIV cohort) and without SIV (non-SIV cohort). All IWSs were deployed successfully, but nine cases (26.4%) of SIV occurred during placement. The mean lesion length was 22.3 cm, and critical limb threatening ischemia was observed in 40.6% of the limbs. The overall 12-month primary patency rate was 78.2%. The non-SIV cohort (25 cases) showed a significantly higher primary patency rate than the SIV cohort (9 cases, 91.7% vs. 41.7%, P = 0.0149). IWS implantation showed acceptable durability in Japanese patients in a real-world setting, however, SIV during IWS placement possibly led to a lower 12-month primary patency rate.