Crossover designs are used by a high proportion of studies investigating the effects of transcranial direct current stimulation (tDCS) on motor learning. These designs necessitate attention to aspects of data collection and analysis to take account of design-related confounds including order, carryover, and period effects. In this systematic review, we appraised the method sections of crossover-designed tDCS studies of motor learning and discussed the strategies adopted to address these factors. A systematic search of 10 databases was performed and 19 research papers, including 21 experimental studies, were identified. Potential risks of bias were addressed in all of the studies, however, not in a rigorous and structured manner. In the data collection phase, unclear methods of randomization, various lengths of washout period, and inconsistency in the counteracting period effect can be observed. In the analytical procedures, the stratification by sequence group was often ignored, and data were treated as if it belongs to a simple repeated-measures design. An inappropriate use of crossover design can seriously affect the findings and therefore the conclusions drawn from tDCS studies on motor learning. The results indicate a pressing need for the development of detailed guidelines for this type of studies to benefit from the advantages of a crossover design.