Background/Objectives: Artificial intelligence (AI)-assisted endoscopic ultrasonography (EUS) diagnostic tools have shown excellent performance in diagnosing gastric mesenchymal tumors. This study aimed to assess whether incorporating clinical and endoscopic factors into AI-assisted EUS classification models based on digital image analysis could improve the diagnostic performance of AI-assisted EUS diagnostic tools. Methods: We retrospectively analyzed the data of 464 patients who underwent both EUS and surgical resection of gastric mesenchymal tumors, including 294 gastrointestinal stromal tumors (GISTs), 52 leiomyomas, and 41 schwannomas. AI-assisted classification models for GISTs and non-GIST tumors were developed utilizing clinical and endoscopic factors and digital EUS image analysis. Results: Regarding the baseline EUS classification models, the area under the receiver operating characteristic (AUC) values of the logistic regression, decision tree, random forest, K-nearest neighbor (KNN), and support vector machine (SVM) models were 0.805, 0.673, 0.781, 0.740, and 0.791, respectively. Using the new classification models incorporating clinical and endoscopic factors into the baseline classification models, the AUC values of the logistic regression, decision tree, random forest, KNN, and SVM models increased to 0.853, 0.715, 0.896, 0.825, and 0.794, respectively. In particular, the random forest and KNN models exhibited significant improvement in performance in Delong’s test (both p < 0.001). Conclusion: The diagnostic performance of the AI-assisted EUS classification models improved when clinical and endoscopic factors were incorporated. Our results provided direction for developing new AI-assisted EUS models for gastric mesenchymal tumors.