Although adequate bowel preparation is essential in screening colonoscopy, patient intolerability to bowel cleansing agents is problematic. Recently, a probiotic mixture solution with bisacodyl emerged to improve patient tolerability. We investigated the efficacy, safety, and patient tolerability profiles of probiotics with bisacodyl versus conventional polyethylene glycol (PEG) solution for bowel preparation for screening colonoscopies in healthy patients in this prospective, randomized, case-control study. In total, 385 volunteers were randomly assigned to receive 2 L of water + 200 mL of probiotic solution (case group, n = 195) or 4 L of PEG solution (control group, n = 190). The efficacy of the bowel cleansing was evaluated using the Ottawa scale system, polyp detection rate, and adenoma detection rate, and the patient tolerability profiles were assessed using a questionnaire. The demographics were not significantly different between groups. When the Ottawa score for each bowel segment was stratified into an adequate vs. inadequate level (Ottawa score ≤ 3 vs. >3), there were no statistical differences between groups in each segment of the colon. There were no significant differences in the polyp and adenoma detection rates between groups (38.42% vs. 32.42, p = 0.30; 25.79% vs. 18.97%, p = 0.11). The case group showed significantly fewer events than the control group, especially nausea, vomiting, and abdominal bloating events. Regarding the overall satisfaction grade, the case group reported significantly more “average” scores (95% vs. 44%, p < 0.001) and were more willing to use the same agents again (90.26% vs. 61.85%, p < 0.001). As patient compliance with bowel preparation agents is associated with an adequate level of bowel cleansing, a probiotic solution with bisacodyl might be a new bowel preparation candidate, especially in patients who show a poor compliance with conventional bowel preparation agents.