This study evaluated the impact of differing false positive (FP) rates in two computer-aided detection (CADe) systems on the clinical effectiveness of artificial intelligence (AI)-assisted colonoscopy. The primary outcomes were adenoma detection rate (ADR) and adenomas per colonoscopy (APC). The ADR in the control, system A (3.2% FP rate), and system B (0.6% FP rate) groups were 44.3%, 43.4%, and 50.4%, respectively, with system B showing a significantly higher ADR than the control group. The APC for the control, A, and B groups were 0.75, 0.83, and 0.90, respectively, with system B also showing a higher APC than the control. The non-true lesion resection rates were 23.8%, 29.2%, and 21.3%, with system B having the lowest. The system with lower FP rates demonstrated improved ADR and APC without increasing the resection of non-neoplastic lesions. These findings suggest that higher FP rates negatively affect the clinical performance of AI-assisted colonoscopy.