Emotional intelligence is an important factor contributing to social adaptation. The current study investigated how salivary testosterone (T) and cortisol (C) levels, cognitive control of emotional conflict processing were associated with children's emotional intelligence (EI). Thirty-four 10- to 11-year-old children were enrolled and instructed to complete questionnaires on emotional intelligence as well as empirical tasks of emotional flanker and Stroop with event-related potential (ERP) recordings. Saliva collection took place on another day without ERP tasks. Results showed that lower T and C levels were associated with higher accuracy in emotional conflict tasks, as well as better emotional intelligence (managing self emotions). In the Stroop task, higher T/C ratios were associated with greater congruency effects of N2 latencies, and lower cortisol levels correlated with stronger slow potential activities (SP). For girls, the correlation between cortisol and emotional utilization was mediated by the SP amplitudes on fearful conflicts in the flanker task (95% CI: -8.64, -0.54, p < 0.050). In conclusion, the current study found the relationship between cortisol and an emotional intelligence ability, emotional utilization, might be mediated by brain activities during emotional conflict resolution processing (SP responses) in preadolescent girls. Future studies could further investigate testosterone-cortisol interaction and its relation with cognitive control of emotion as underlying mechanisms of emotional intelligence.