We explored the large variability in motor skill acquisition-related effects on the primary and sensory cortices. Namely, we tested whether this variability depends on interindividual variance or the type of motor task investigated. We compared different motor-learning tasks, i.e. model-free vs. model-based learning tasks, and their possible differential effects on the primary motor and sensory cortices by using transcranial magnetic stimulation techniques. The model-free learning task induced an increase in corticospinal excitability and a reduction in the amplitude of somatosensory-evoked potentials. Conversely, the model-based learning tasks induced a decrease in intracortical inhibition. No correlations were found between neurophysiological changes and motor performance, indicating that this differential modulation may be secondary to the motor skill acquisition. The study results suggest differential motor skill acquisition-related effects on cortical parameters, possibly due to the engagement of specific neurophysiological substrates. A large variability in learning-related neurophysiological changes in the primary motor and sensory cortices has been observed. It is unclear whether these differential effects are due to the different tasks investigated or to interindividual variance. Only a few studies have assessed different motor-learning tasks and their effects on neurophysiological features within the same group of participants, and several issues are unclear. Here, we compared the effects of different tasks within each individual. We investigated the effects on motor and sensory cortex parameters after a model-free learning task, i.e. a ballistic motor task, compared with model-based learning tasks, i.e. visuomotor-learning tasks. Motor- and sensory-evoked potentials, intracortical excitability as assessed by short-interval intracortical inhibition, and sensorimotor interaction, i.e. short-latency afferent inhibition, were recorded from 15 healthy subjects before and after the tasks. The ballistic motor task induced an increase in corticospinal excitability but did not change motor cortex intracortical inhibition or sensorimotor integration. In addition, it decreased the amplitude of cortical components of the somatosensory-evoked potentials. The visuomotor-learning tasks induced a reduction in motor cortex intracortical inhibition but did not modulate corticospinal and sensory cortex excitability or sensorimotor integration. This differential modulation is likely to be secondary to the motor skill acquisition, since no correlation was observed between neurophysiological changes and motor performance. Our results demonstrate differential motor skill acquisition-related effects on cortical parameters, possibly reflecting the engagement of specific neurophysiological substrates, and contribute in-depth knowledge of the mechanisms involved in different types of motor skill acquisition in humans.