The serotonin transporter plays an important role in serotonergic neuromodulation. It is known that polymorphisms in the serotonin transporter gene are linked to the dysregulation of emotions. In the current study, we aimed to investigate the impact of variation in the gene encoding serotonin transporter polymorphism on oscillatory dynamics during inhibition of planned movement in the stop signal paradigm. During performance the stop signal paradigm, electroencephalograms (EEGs) were recorded in 90 healthy Caucasian children (39 girls) from 7 to 12 years. Buccal epithelium probes were taken from all participants. The La, Lg, and S alleles of serotonin transporter‐linked polymorphic region (5‐HTTLPR) polymorphism were detected in the DNA samples using PCR. LaLa genotype carriers did not differ from LaS\LgS and LgS\LgLg\SS carriers in a number of successful inhibitions of a prepotent response. Carriers of LaLa exhibit higher alpha and beta event‐related spectral perturbations (ERSP) in parietal and occipital cortices after the presentation of signal of inhibition of movement than LaS\LgS and LgS\LgLg\SS carriers. Results are consistent with current literature and confirm that S allele carriers are more predisposed to disturbances in cognitive control.