Objectives: Endovascular repair (ER) of popliteal artery aneurysm (PAA) is an alternative to open repair. However, there is no standardized protocol for when to opt for ER and the decision is therefore at the discretion of the clinician. This study aims to evaluate the adherence to the Instruction For Use (IFU) in patients undergoing ER for PAA and factors associated with stent graft patency at one year. Methods: The adherence to IFU provided by the manufacturer in 55 patients treated with Gore Viabahn® Endoprosthesis with Heparin Bioactive Surface for PAA between 2009 and 2019 were retrospectively analyzed. Duplex follow-up was performed at 30 days and one year. Results: The two groups of patients treated within (n = 10) and not within (n = 45) IFU did not differ in patient demographics, diagnostic assessment, treatment or outcome. Forty-five patients (81.8%) received stent graft placement with at least one deviation according to IFU. Distal oversizing >20% was the most frequent deviation against IFU (n = 22, 40.0%). Primary patency at one year was 72%. Diameter size difference >1 mm between overlapping stent grafts (6/14 [43%], p = 0.013) and renal insufficiency (5/12 [42%], p = 0.0086) were associated with lower primary patency at one year. Age-adjusted analysis of tortuosity index (HR 1.78/SD, 95% CI 1.17–2.71; p = 0.0071) and maximal PAA angle (HR 1.73/SD, 95% CI 1.018–2.95; p = 0.043) were associated with major amputation/mortality at end of follow-up. Conclusion: The majority of patients undergoing ER for PAA were not treated within IFU. Diameter size difference >1 mm between overlapping stent grafts was associated with a higher loss of primary patency at one year. Multi-center studies with larger sample size and long-term follow up of patency are warranted.