Standard precautions protect patients and nurses from infection. Nevertheless, compliance with standard precautions is lower among emergency department nurses than other nurses. We examined the individual and organizational factors that influence emergency department nurses’ compliance with standard precautions via a cross-sectional study. A self-reported questionnaire survey was administered to 140 nurses working in nine emergency departments in South Korea. It included items regarding ethical awareness and standard precaution self-efficacy at the individual level as well as safety environment, organizational culture for infection control, and degree of compliance with standard precautions at the organizational level. Individual and organizational predictors were identified using a multilevel analysis. The results indicated that 81.1% of nurses’ compliance with standard precautions was influenced by individual differences, while only 18.9% was influenced by organizational differences. Individual- and organizational-level predictors explained 46.7% and 55.4% of the variance in emergency department nurses’ compliance with standard precautions, respectively. Emergency department nurses’ compliance with standard precautions was predicted by ethical awareness and standard precaution self-efficacy at the individual level and by organizational culture for infection control at the organizational level. Our findings provide evidence for the need to improve facilities and human resource management as well as the organizational culture for infection control.