The neurobiological underpinnings of insomnia disorder (ID) are still poorly understood. A previous meta-analysis conducted by our research group in 2018 revealed no consistent regional alterations based on the limited number of eligible studies. Given the number of studies published during the last few years, we revisited the meta-analysis to provide an update to the field. Following the best-practice guidelines for conducting neuroimaging meta-analyses, we searched several databases (PubMed, Web of Science, and BrainMap) and identified 39 eligible structural and functional studies, reporting coordinates reflecting significant group differences between ID patients and healthy controls. A significant convergent regional alteration in the subgenual anterior cingulate cortex (sgACC) was observed using the activation likelihood estimation algorithm. Behavioural decoding using the BrainMap database indicated that this region is involved in fear-related emotional and cognitive processing. The sgACC showed robust task-based co-activation in meta-analytic connectivity modelling and task-free functional connectivity in a resting-state functional connectivity analysis with the main hubs of the salience and default mode networks, including the posterior cingulate cortex and dorsal ACC, amygdala, hippocampus, and medial prefrontal cortex. Collectively, the findings from this large-scale meta-analysis suggest a critical role of the sgACC in the pathophysiology of ID.