Various brain regions contribute to aspects of attentional control in conflict resolution. Here, we used transcranial magnetic stimulation (TMS) to examine the functions of posterior parietal cortex (PPC) and dorsal medial frontal cortex (dMFC) in a visual flanker task. Participants responded to a central target that was flanked by congruent, neutral or incongruent stimuli on the left or right. Offline low-frequency repetitive TMS (1 Hz, 110% motor threshold, 20 min) was applied to right PPC or dMFC. Performance, as measured by reaction times and accuracy, was established at baseline, after rTMS, and sham stimulation before or after active rTMS. After rTMS to right PPC, the interference of flankers presented in the left visual hemispace diminished selectively. By contrast, after rTMS over the right dMFC, flanker effects in both visual fields remained. Our results suggest that right PPC specifically contributes to the assignment of spatial attention during stimulus encoding.