Sensory rhythmic stimulation enhances executive functions by entraining oscillations in higher-order cortical networks, but its effects on subcortical structures remain unclear. We propose that stimulus valence is a key feature to enable subcortical entrainment. Using intracranial EEG in epileptic patients, we first show that visual search is supported by cortico-subcortical theta (5Hz) activity. We then show that 5 Hz negative-valence visual stimulation entrains theta oscillations in a task-related network, including the ventral visual stream, hippocampus, and dorsolateral prefrontal cortex. Finally, in a behavioral experiment in healthy individuals, we show that both neutral and negative valence 5 Hz stimulation improved visual search speed, but only negative valence stimulation enhanced target image recognition as assessed through an additional memory task. These findings highlight the role of stimulus valence in modulating subcortical brain activity and behaviors through rhythmic sensory stimulation and pave the way for further applications in clinical intervention.