Background Since the introduction of the Critical View of Safety approach in laparoscopic cholecystectomy, exposure of the common bile duct, and common hepatic duct is not recommended, therefore, the length of the cystic duct remnant is no longer controlled. The aim of this case‒control study is to evaluate the relationship between the length of the cystic duct remnant and the risk for bile duct stone recurrence after cholecystectomy. Methods All MRIs with dedicated sequences of the biliary tract taken between 2010 and 2020 from patients who underwent prior cholecystectomy were reviewed. The length of the cystic duct remnant was measured and compared between the patients with and without bile duct stones using multivariate logistic regression analysis. Results A total of 362 patients were included in this study, 23.5% of whom had bile duct stones on MRI. The cystic duct remnant was significantly longer in the patients with stones than in the control group (median 31 mm versus 18 mm, P < 0.001). In the MRIs performed > 2 years after cholecystectomy, the cystic duct remnant was also significantly longer in the patients with bile duct stones (median 32 mm versus 21 mm, P < 0.001). A cystic duct remnant ≥ 15 mm in length increased the odds of stones (OR = 2.3, P = 0.001). Overall, the odds of bile duct stones increased with an increasing cystic duct remnant length (≥ 45 mm, OR = 5.0, P < 0.001). Conclusions An excessive cystic duct remnant length increases the odds of recurrent bile duct stones after cholecystectomy.