BACKGROUND: Video capsule endoscopy (VCE) is a noninvasive technique used to examine small bowel abnormalities in both adults and children. However, manual review of VCE images is time-consuming and labor-intensive, making it crucial to develop deep learning methods to assist in image analysis. AIM: To employ deep learning models for the automatic classification of small bowel lesions using pediatric VCE images. METHODS: We retrospectively analyzed VCE images from 162 pediatric patients who underwent VCE between January 2021 and December 2023 at the Children's Hospital of Nanjing Medical University. A total of 2298 high-resolution images were extracted, including normal mucosa and lesions (erosions/erythema, ulcers, and polyps). The images were split into training and test datasets in a 4:1 ratio. Four deep learning models: DenseNet121, Visual geometry group-16, ResNet50, and vision transformer were trained using 5-fold cross-validation, with hyperparameters adjusted for optimal classification performance. The models were evaluated based on accuracy, precision, recall, F1-score, and area under the receiver operating curve (AU-ROC). Lesion visualization was performed using gradient-weighted class activation mapping. RESULTS: Abdominal pain was the most common indication for VCE, accounting for 62% of cases, followed by diarrhea, vomiting, and gastrointestinal bleeding. Abnormal lesions were detected in 93 children, with 38 diagnosed with inflammatory bowel disease. Among the deep learning models, DenseNet121 and ResNet50 demonstrated excellent classification performance, achieving accuracies of 90.6% [95% confidence interval (CI): 89.2-92.0] and 90.5% (95%CI: 89.9-91.2), respectively. The AU-ROC values for these models were 93.7% (95%CI: 92.9-94.5) for DenseNet121 and 93.4% (95%CI: 93.1-93.8) for ResNet50. CONCLUSION: Our deep learning-based diagnostic tool developed in this study effectively classified lesions in pediatric VCE images, contributing to more accurate diagnoses and increased diagnostic efficiency.