Stimulus-induced conflicts in decision-making tasks produce both behavioral and neuronal congruency effects. However, how and when conflicts are detected and resolved at the neuronal level remains largely unclear. To address these issues, we recorded from single neurons in the frontal eye fields of two macaques performing a conflict task. Although the temporal dynamics of the neuronal congruency effects are independent of the specific task rules, they are substantially different in target- and distractor-encoding neurons. Conflicts were detected ~100 ms after the conflict-inducing cue (20-30 ms after the visual response), which is much faster than predicted based on human EEG results. This suggests that conflict detection relies on a fast mechanism in frontal eye fields. Resolving the conflict at the neuronal level, however, requires between <400 ms to ~1000 ms, and shows profound interindividual differences and depends on task rules, indicating that it is a more complex and top-down driven process. Our findings illuminate the neuronal mechanisms underlying decision-making when a conflict is present, a crucial cognitive process playing a role in basic survival and high-level cognitive functions.