A standardized small bowel (SB) cleansing scale is currently not available. The aim of this study was to develop an automated calculation software for SB cleansing score using deep learning. Consecutively performed capsule endoscopy cases were enrolled from three hospitals. A 5-step scoring system based on mucosal visibility was trained for deep learning in the training set. Performance of the trained software was evaluated in the validation set. Average cleansing score (1.0 to 5.0) by deep learning was compared to clinical grading (A to C) reviewed by clinicians. Cleansing scores decreased as clinical grading worsened (scores of 4.1, 3.5, and 2.9 for grades A, B, and C, respectively, P < 0.001). Adequate preparation was achieved for 91.7% of validation cases. The average cleansing score was significantly different between adequate and inadequate group (4.0 vs. 2.9, P < 0.001). ROC curve analysis revealed that a cut-off value of cleansing score at 3.25 had an AUC of 0.977. Diagnostic yields for small, hard-to-find lesions were associated with high cleansing scores (4.3 vs. 3.8, P < 0.001). We developed a novel scoring software which calculates objective, automated cleansing scores for SB preparation. The cut-off value we suggested provides a standard criterion for adequate bowel preparation as a quality indicator.