Left and right prefrontal cortex and the primary motor cortex (M1) are activated during learning of motor sequences. Previous literature is mixed on whether prefrontal cortex aids or interferes with sequence learning. The present study investigated the roles of prefrontal cortices and M1 in sequence learning. Participants received anodal transcranial direct current stimulation (tDCS) to right or left prefrontal cortex or left M1 during a probabilistic sequence learning task. Relative to sham, the left prefrontal cortex and M1 tDCS groups exhibited enhanced learning evidenced by shorter response times for pattern trials, but only for individuals who did not gain explicit awareness of the sequence (implicit). Right prefrontal cortex stimulation in participants who did not gain explicit sequence awareness resulted in learning disadvantages evidenced by slower overall response times for pattern trials. These findings indicate that stimulation to left prefrontal cortex or M1 can lead to sequence learning benefits under implicit conditions. In contrast, right prefrontal cortex tDCS had negative effects on sequence learning, with overall impaired reaction time for implicit learners. There was no effect of tDCS on accuracy, and thus our reaction time findings cannot be explained by a speed-accuracy tradeoff. Overall, our findings suggest complex and hemisphere-specific roles of left and right prefrontal cortices in sequence learning. NEW & NOTEWORTHY Prefrontal cortices are engaged in motor sequence learning, but the literature is mixed on whether the prefrontal cortices aid or interfere with learning. In the current study, we used anodal transcranial direct current stimulation to target left or right prefrontal cortex or left primary motor cortex while participants performed a probabilistic sequence learning task. We found that left prefrontal and motor cortex stimulation enhanced implicit learning whereas right prefrontal stimulation negatively impacted performance.