Stimulus-induced conflicts in decision making tasks produce both behavioral and neuronal congruency effects (NCE). However, how and when conflicts are detected and resolved at neuronal level remains largely unclear. To address these issues, we recorded from single neurons in the frontal eye fields (FEF) of two macaques performing a conflict task. We found temporal dynamics of the NCEs are independent of the specific task rules, yet they are substantially different in target- and distractor-encoding neurons. Conflicts were detected ~100ms after the conflict-inducing cue (20-30ms after the visual response), which is much faster than predicted based on human EEG results. This suggest that conflict detection by FEF neurons is an automatic and bottom-up driven process. Resolving the conflict at neuronal level, however, requires between <400ms to ~1000ms, and shows profound interindividual differences and depends on task rules, indicating that it is a more complex and top-down driven process.