Small bowel capsule endoscopy (SBCE) is a convenient and minimally invasive method widely used to evaluate the small intestine. However, especially in the distal ileum, visualization of the intestinal mucosa is frequently hampered by the remaining intestinal contents, making it difficult to detect critical lesions. Although several studies have reported on the efficacy of bowel preparation before SBCE, no standardized protocol has been established. Herein, we determined the optimal preparation method for better visualization of the distal ileum using SBCE. We retrospectively analyzed 259 consecutive patients who had undergone SBCE between July 2009 and December 2019, divided into three groups: Group A (no preparation except overnight fasting), Group B (ingestion of 1–2 L polyethylene glycol 4 h before colonoscopy after overnight fasting and performing SBCE immediately after colonoscopy), and Group C (ingestion of 0.9 L magnesium citrate [MC] before SBCE after overnight fasting). The visibility of the intestinal mucosa in the first 10 min and at the last 10 min during the period of observation of the distal ileum was examined using a scoring system and compared. The visibility of the images captured by SBCE was assessed based on the scoring of the degree of bile/chyme staining, residual fluid and debris, brightness, bubble reduction, and visualized mucosa. The status of intestinal collapse was also assessed. In the first 10 min of observation of the distal ileum, no significant differences were detected among the groups. In the last 10 min, significantly better images were acquired in Group C in terms of bile/chyme staining, brightness, bubble reduction, and visualized mucosa. Bowel preparation using a low-dose MC solution 2 h before SBCE provided significantly higher-quality images of the distal ileum. Further optimization, such as the timing of initiating the preparation, is necessary to determine the optimal regimen for bowel preparation prior to SBCE.