To evaluate efficacy of the AIxURO system, a deep learning-based artificial intelligence (AI) tool, in enhancing the accuracy and reliability of urine cytology for diagnosing upper urinary tract cancers. One hundred and eighty-five cytology samples of upper urine tract were collected and categorized according to The Paris System for Reporting Urinary Cytology (TPS), yielding 168 negative for High-Grade Urothelial Carcinoma (NHGUC), 14 atypical urothelial cells (AUC), 2 suspicious for high-grade urothelial carcinoma (SHGUC), and 1 high-grade urothelial carcinoma (HGUC). The AIxURO system, trained on annotated cytology images, was employed to analyze these samples. Independent assessments by a cytotechnologist and a cytopathologist were conducted to validate the initial AIxURO assessment. AIxURO identified discrepancies in 37 of the 185 cases, resulting in a 20% discrepancy rate. The cytotechnologist achieved an accuracy of 85% for NHGUC and 21.4% for AUC, whereas the cytopathologist attained accuracies of 95% for NHGUC and 85.7% for AUC. The cytotechnologist exhibited overcall rates of roughly 15% and undercall rates of greater than 50%, while the cytopathologist showed profoundly lower miscall rates from both undercall and overcall. AIxURO significantly enhanced diagnostic accuracy and consistency, particularly in complex cases involving atypical cells. AIxURO can improve the accuracy and reliability of cytology diagnosis for upper urine tract urothelial carcinomas by providing precise detection on atypical urothelial cells and reducing subjectivity in assessments. The integration of AIxURO into clinical practice can significantly ameliorate diagnostic outcomes, highlighting the synergistic potential of AI technology and human expertise in cytology.