To examine the association between electronic prescribing of controlled substances (EPCS) and controlled substance prescription patterns in U.S. emergency departments (ED). We conducted cross-sectional analysis at both the ED level and visit level, using the 2016-2017 National Hospital Ambulatory Medical Care Surveys. The sample included 24,296 visits to 316 EDs, 45% of which utilized EPCS. Pain-related visits were associated with significantly higher odds of prescriptions for any controlled substances (OR = 1.52; 95% CI: 1.32-1.75; p < 0.001) and Schedule II substances (OR = 2.13; 95% CI: 1.80-2.52; p < 0.001). Conditional on pain-related visits, EPCS was significantly associated with higher odds of any (OR 1.31; 95% CI: 1.08-1.59; p = 0.006) and Schedule III (OR 1.38; 95% CI: 1.03-1.85; p = 0.031) controlled substance prescriptions. For non-pain related visits, EPCS was not associated with changes in controlled substance prescriptions. While EPCS transmits prescriptions directly to pharmacies in order to reduce drug diversion problems, the results indicated no significant association between EPCS use and prescriptions for Schedule II drugs which include opioids. As many states move towards mandating EPCS use in order to curb the opioid epidemic, future studies should examine the barriers to the effective implementation of EPCS, in the context of other systems such as Prescription Drug Monitoring Programs. EPCS does not appear to deter Schedule II controlled substances prescription including opioids in an ED visit. It may facilitate any and Schedule III controlled substance prescriptions when pain was involved in an ED visit.