Many studies have implicated the dorsolateral prefrontal cortex in the acquisition of skill, including procedural sequence learning. However, the specific role it performs in sequence learning has remained uncertain. This type of skill has been intensively studied using the serial reaction time task. We used three versions of this task: a standard task where the position of the stimulus cued the response; a non-standard task where the color of the stimulus was related to the correct response; and a combined task where both the color and position simultaneously cued the response. We refer to each of these tasks based upon the cues available for guiding learning as position, color and combined tasks. The combined task usually shows an enhancement of skill acquisition, a result of being driven by two simultaneous and congruent cues. Prior to the performance of each of these tasks the function of the dorsolateral prefrontal cortex was disrupted using repetitive transcranial magnetic stimulation. This completely prevented learning within the position task, while sequence learning occurred to a similar extent in both the color and combined tasks. So, following prefrontal stimulation the expected learning enhancement in the combined task was lost, consistent with only a color cue being available to guide sequence learning in the combined task. Neither of these effects was observed following stimulation at the parietal cortex. Hence the critical role played by the dorsolateral prefrontal cortex in sequence learning is related exclusively to spatial cues. We suggest that the dorsolateral prefrontal cortex operates over the short term to retain and manipulate spatial information to allow cortical and subcortical structures to learn a predictable sequence of actions. Such functions may emerge from the broader role the dorsolateral prefrontal cortex has in spatial working memory. These results argue against the dorsolateral prefrontal cortex constituting part of the neuronal substrate responsible for general aspects of implicit or explicit sequence learning.