The lateral prefrontal cortex (lPFC) is reliably active during working memory (WM) across human and animal models, but the role of lPFC in successful WM is under debate. For instance, non-human primate (NHP) electrophysiology research finds that lPFC circuitry stores WM representations. Human neuroimaging instead suggests that lPFC plays a control function over WM content that is stored in sensory cortices. These seemingly incompatible WM accounts are often confounded by differences in the amount of task training and stimulus exposure across studies (i.e., NHPs tend to be trained extensively). Here, we test the possibility that such long-term training may alter the role of lPFC in WM maintenance. We densely sampled WM-related activity across learning, in three human participants, using a longitudinal functional MRI (fMRI) protocol. Over three months, participants trained on (1) a serial reaction time (SRT) task, wherein complex fractal stimuli were embedded within probabilistic sequences, and (2) a delayed recognition task probing WM for trained or novel stimuli. Participants were scanned frequently throughout training, to track how WM activity patterns change with repeated stimulus exposure and long-term associative learning. WM task performance improved for trained (but not novel) fractals and, neurally, delay activity significantly increased in distributed lPFC voxels across learning. Pattern similarity analyses also found that item-level WM representations emerged within lPFC, but not in sensory cortices, and lPFC delay activity increasingly reflected sequence relationships from the SRT task, even though that information was task-irrelevant for WM. These findings demonstrate that human lPFC develops stimulus-selective WM responses with learning and WM representations are shaped by long-term experience. Influences from training and long-term memory may reconcile competing accounts of lPFC function during WM.