Background Recent studies have shown that neurophysiological outcomes of transcranial direct current stimulation (TDCS) are influenced by current flow in brain regions between the electrodes, and in particular the orientation of current flow relative to the cortical surface. Objective We asked whether the directional effects of TDCS on physiological measures in the motor system would also be observed on motor behaviours. Methods We applied TDCS during the practice of a ballistic movement task to test whether it affected learning or the retention of learning 48 h later. TDCS electrodes were oriented perpendicular to the central sulcus and two current orientations were used (posterior-anterior, TDCS PA ; and anterior-posterior, TDCS AP ). Transcranial magnetic stimulation (TMS) was used to assess whether changes in corticospinal excitability reflected any behavioural changes. Results Directional TDCS AP impaired the retention of learning on the ballistic movement task compared to TDCS PA and a sham condition. Although TDCS PA had no effect on learning or retention, it blocked the typical increase in corticospinal excitability after a period of motor practice. Conclusions Our results extend on previous reports of TDCS producing directionally specific changes in neurophysiological outcomes by showing that current direction through a cortical target also impacts upon behavioural outcomes. In addition, changes in corticospinal excitability after a period of motor practice are not causally linked to behavioural learning.