Background: A variety of pathophysiological changes in the biliary system occur in patients with cholelithiasis, but the changes in the bile flow dynamics in those patients remain unclear. The purpose of this study was to elucidate the changes in the bile flow dynamics in patients with cholelithiasis using cine-dynamic magnetic resonance cholangiopancreatography (MRCP) with a spatially selective inversion-recovery (IR) pulse. Methods: We retrospectively examined 25 patients with gallstones (gallstone group) and 69 patients without gallstones (non-gallstone group) who underwent abdominal MRI, including in- and opposed-phase T1-weighted images and cine-dynamic MRCP with a spatially selective IR pulse. The frequency and secretion grade of the antegrade and reverse flow of the bile on the cine dynamic MRCP images and the signal intensity ratio (SIR) of the gallbladder in the in- and opposed-phase T1-weighted images were evaluated. Results: The frequency and mean secretion grade of the antegrade bile flow were significantly higher in the gallstone group than in the non-gallstone group (p = 0.011 and p = 0.003), while no significant differences in those values of the reverse bile flow were found between the two groups. The SIR of the gallbladder in the T1-weighted gradient-echo in-phase images was significantly lower in the gallstone group than in the non-gallstone group (p = 0.004). Conclusions: Cine-dynamic MRCP with a spatially selective IR pulse can noninvasively visualize changes in the bile flow dynamics of patients with gallstones.