Background Gallstones are known to occur quite frequently after gastrectomy. Most of the studies about postoperative cholelithiasis have focused on open gastrectomy, whereas laparoscopic gastrectomy has recently gained popularity as a type of minimally invasive surgery (MIS). Hence, the efficacy of MIS in preventing post-gastrectomy gallstone formation remains to be elucidated. This study aimed to evaluate the risk of gallstone formation after MIS for clinical stage I/IIA gastric cancer. Methods A total of 1166 patients undergoing gastrectomy for clinical stage I/IIA gastric cancer between 2009 and 2016 were included in this study. Gallstones were detected on abdominal ultrasound and/or computed tomography. Multivariate logistic regression analysis was used to determine factors associated with postoperative gallstone formation. Results Gallstone formation was observed in 174 patients (15%), of whom 22 (2%) experienced symptomatic cholelithiasis. In multivariate analysis, the following were identified as risk factors for post-gastrectomy gallstone formation: open approach with an odds ratio (OR) of 1.670 and a 95% confidence interval (CI) of 1.110–2.510 ( P  = 0.014), older age (OR 1.880; 95% CI 1.290–2.730; P  < 0.001), high body mass index (OR 1.660; 95% CI 1.140–2.420; P  = 0.008), Roux-en-Y (RY) reconstruction (OR 1.770; 95% CI 1.230–2.530; P  = 0.002), hepatic branch vagotomy (OR 1.600; 95% CI 1.050–2.440; P  = 0.029), and intra-abdominal infectious complications (OR 3.040; 95% CI 1.680–5.490; P  < 0.001). Conclusion Our study suggested that MIS along with the preservation of the hepatic vagus nerve and non-RY reconstruction could help prevent post-gastrectomy gallstone development.