The frontal eye field (FEF) and the inferior frontal junction (IFJ) are prefrontal structures involved in mediating multiple aspects of goal-driven behavior. Despite being recognized as prominent nodes of the networks underlying spatial attention and oculomotor control, and working memory and cognitive control, respectively, the limited quantitative evidence on their precise localization has considerably impeded the detailed understanding of their structure and connectivity. In this study, we performed an activation likelihood estimation (ALE) fMRI meta-analysis by selecting studies that employed standard paradigms to accurately infer the localization of these regions in stereotaxic space. For the FEF, we found the highest spatial convergence of activations for prosaccade and antisaccade paradigms at the junction of the precentral sulcus and superior frontal sulcus. For the IFJ, we found consistent activations across oddball/attention, working memory, task-switching and Stroop paradigms at the junction of the inferior precentral sulcus and inferior frontal sulcus. We related these clusters to previous meta-analyses, sulcal/gyral neuroanatomy, and a comprehensive brain parcellation, highlighting important differences compared to their results and taxonomy. Finally, we leveraged the ALE peak coordinates as seeds to perform a meta-analytic connectivity modeling (MACM) analysis, which revealed systematic coactivation patterns spanning the frontal, parietal, and temporal cortices. We decoded the behavioral domains associated with these coactivations, suggesting that these may allow FEF and IFJ to support their specialized roles in flexible behavior. Our study provides the meta-analytic groundwork for investigating the relationship between functional specialization and connectivity of two crucial control structures of the prefrontal cortex.