Transcranial magnetic stimulation (TMS) allows non-invasive manipulation of brain activity during active task performance. Because every TMS pulse is accompanied by non-neural effects such as a clicking sound and somato-sensation on the head, control conditions are required to ensure that changes in task behavior are indeed due to the induced neural effects. However, the non-neural effects of TMS in the context of a given task performance are largely unknown and, consequently, it is unclear what constitutes a valid control condition. We explored the non-neural effects of TMS on visual target detection. Participants received single pulse sham TMS to each hemisphere at different time points prior to target appearance during a visual target detection task. It was hypothesized that the clicking sound of a sham TMS pulse differentially affects performance depending on the location of the coil and the timing of the pulse.Our results show that, first, sham TMS caused a facilitation of reaction times when preceding the target stimulus by 150, 200, and 250 ms, whereas earlier and later time windows were not effective. Second, positioning the TMS coil ipsilateral instead of contralateral relative to the target stimulus improved reaction times. Third, infrequent noTMS trials that were interleaved with sham TMS trials had oddball-like properties resulting in increased reaction times during noTMS. The clicking sound produced by sham TMS influences task performance in multiple ways. These non-neural effects of TMS need to be controlled for in TMS research and the present findings provide an empirical basis for deciding what constitutes a valid control condition.