Transcranial direct current stimulation (tDCS) over the primary motor cortex (M1) can facilitate motor learning, but it has not been established how stimulation to other brain regions impacts online and offline motor sequence learning, as well as long-term retention. Here, we completed three experiments comparing the effects of tDCS and sham stimulation to the prefrontal cortex (PFC), M1, and the supplementary motor area complex to understand the contributions of these brain regions to motor sequence learning. In Experiment 1, we found that both left and right PFC tDCS groups displayed a slowing in learning in both reaction time and number of chunks, whereas stimulation over M1 improved both metrics over the course of three sessions. To better understand the sequence learning impairment of left PFC anodal stimulation, we tested a left PFC cathodal tDCS group in Experiment 2. The cathodal group demonstrated learning impairments similar to the left PFC anodal stimulation group. In Experiment 3, a subset of participants from the left PFC, M1, and sham tDCS groups of Experiment 1 returned to complete a single session without tDCS on the same sequences assigned to them 1 year previously. We found that the M1 tDCS group reduced reaction time at a faster rate relative to the sham and left PFC groups, demonstrating faster relearning after a one-year delay. Thus, our findings suggest that, regardless of the polarity of stimulation, tDCS to PFC impairs sequence learning, whereas stimulation to M1 facilitates learning and relearning, especially in terms of chunk formation.