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Startling acoustic stimulation (SAS) causes a transient effect on the primary motor cortex (M1) nonreflexively. It reduces the cortical excitability at rest, but not during voluntary contraction. However, the effect of SAS on intracortical activity is not clear. The purpose of this study was to investigate the SAS effect on short-interval intracortical inhibition and intracortical facilitation using transcranial magnetic stimulation (TMS). Eleven healthy individuals performed isometric elbow flexion at 10% of maximum voluntary contraction on the dominant side with a real-time visual target (i.e., M1 preactivation) or at rest. TMS was delivered to the M1 ipsilateral to elbow flexion without or with SAS delivered 90 ms prior to TMS. There were three TMS delivery conditions: (a) single pulse, (b) short-interval intracortical inhibition, and (c) intracortical facilitation. TMS-induced motor-evoked potential (MEP) was compared between predetermined TMS and SAS conditions at rest and during ipsilateral voluntary contraction. We confirmed that SAS decreased the MEP amplitude at rest, but not during M1 preactivation. SAS caused task-specific effects on intracortical excitability. Specifically, SAS increased intracortical facilitation at rest and during voluntary contraction. However, SAS decreased short-interval intracortical inhibition only during M1 preactivation. Collectively, our results suggest that SAS transiently influences the motor cortex excitability, possibly via its activation of higher centers, to achieve a visually guided goal-directed task.