Prospective enrollment of research subjects in the fast-paced emergency department (ED) is challenging. We sought to develop a software application to increase real-time clinical trial enrollment during an ED visit. The Prospective Intelligence System for Clinical Emergency Services (PISCES) scans the electronic health record during ED encounters for preselected clinical characteristics of potentially eligible study participants and notifies the treating physician via mobile phone text alerts. PISCES alerts began 3 months into a cluster randomized trial of an electronic health record-based risk stratification tool for pediatric abdominal pain in 11 Northern California EDs. We compared aggregate enrollment before (2577 eligible patients, October 2016 to December 2016) and after (12 049 eligible patients, January 2017 to January 2018) PISCES implementation. Enrollment increased from 10.8% to 21.1% following PISCES implementations (P < .001). PISCES significantly increased study enrollment and can serve as a valuable tool to assist prospective research enrollment in the ED.