In children and adolescents, 1 mA transcranial direct current stimulation (tDCS) may cause “paradoxical” effects compared with adults: both 1 mA anodal and cathodal tDCS increase amplitude of the motor evoked potential (MEP) as revealed by a single pulse transcranial magnetic stimulation (TMS) of the motor cortex. Here, EEG based evoked potentials induced by a single pulse TMS, particularly the N100 component as marker of motor cortex inhibition, were investigated in order to explain effects of tDCS on the developing brain. In nineteen children and adolescents (11–16 years old), 1 mA anodal, cathodal, or sham tDCS was applied over the left primary motor cortex for 10 min. The TMS-evoked N100 was measured by 64-channel EEG before and immediately after stimulation as well as every 10 min after tDCS for one hour. 1 mA Cathodal stimulation suppressed the N100 amplitude compared with sham stimulation. In contrast, anodal tDCS did not modify the N100 amplitude. It seems likely that the increase of the motor cortex activity under cathodal tDCS in children and adolescents as shown in previous studies can be attributed to a reduce inhibition. Based on TMS evoked N100, the study provides an insight into neuromodulatory effects of tDCS on the developing brain.