Background The interhemispheric difference in cortical excitability and its relationship to motor functions is unclear. Aim We examined the relationship between handedness, left and right motor cortex excitability and fine and gross motor functions in adolescence. Methods 28 healthy adolescents (age 16–19 years, 19 girls) were studied. Handedness was determined by the Waterloo Handedness Questionnaire. Motor threshold (MT) of the abductor pollicis brevis was measured on both hemispheres using biphasic stimulation, and on the left hemisphere also with monophasic stimulation. Box and block test (BBT) was used for manual dexterity, line run and standing long jump for gross motor tasks. Spearman correlations and paired samples t -test were used. Results All subjects were right-handed; handedness score varied between 16 and 40. MT of the left hemisphere assessed with monophasic stimulation correlated with handedness (−0.516, p = 0.006) and remained a trend with biphasic waveform (−0.353, p = 0.065). MT was not different between hemispheres (40.3 in the left vs. 41.3% in the right hemisphere). BBT result was better with right hand (76.7 vs 73.9, p = 0.008). MT of the right hemisphere correlated with the BBT of the right hand ( r = −0.383, p = 0.044). MTs and gross motor tasks did not correlate. Discussion On the right, non-dominant hemisphere, higher excitability was associated with better ipsilateral performance. Gross motor functions may be more strongly related to muscle force and therefore do not correlate with cortical excitability. Clearly established right-handedness is related to higher excitability in the dominant hemisphere. Interestingly, this seems to partly depend on the stimulation type.