Neuroimaging and behavioral evidence has suggested that the lateral prefrontal cortex is involved in individual differences in working memory capacity (WMC). However, few studies have localized the neural structures that differentiate high and low WMC individuals, considering the functional architecture of the prefrontal cortex. The present study aimed to identify a frontal region that underlies individual differences from the perspective of the hierarchical architecture of the frontal cortex. By manipulating an episodic factor of cognitive control (control in selecting an appropriate task set according to a temporal context) and using a parametric modulation analysis, we found that both high- and low- WMC individuals have similar activation patterns in the premotor cortex (BA6, 8), caudal prefrontal cortex (BA44, 45), and frontopolar cortex (BA10, 11), but differed in the rostral part of the prefrontal cortex (BA46/47); high WMC individuals showed greater activation in the higher episodic control condition, whereas low WMC individuals showed reduced activation when episodic control was required. Similar patterns of activation were found in the right inferior parietal and middle/inferior temporal cortices. These results indicate that the rostral prefrontal cortex, which supports episodic cognitive control, possibly by sending a weighting signal toward the inferior parietal and middle/inferior temporal cortices that modulate saliency and sensory processing, underlies individual differences in WMC. Episodic control account, which considers the organization of the prefrontal cortex, fits well with previous findings of individual differences in WMC.