Maladaptive implicit emotion regulation has been highlighted as a transdiagnostic characteristic of mood and anxiety disorders. Whilst clinical diagnosis has relied on signs and symptoms, the integration of clinical neurosciences is becoming more important as a means of enhancing assessment, diagnosis, and treatment. Thus, activation likelihood estimation (ALE) meta-analysis was conducted for whole-brain foci comparing implicit emotion regulation in a large sample of patients with mood and anxiety disorders and healthy controls. Twenty-four clinical studies were identified based on established criteria (e.g., DSM-5). ALE meta-analysis reported convergence of hypoactivation in patients (n = 432) in the right medial frontal gyrus (BA9), spreading to the right anterior cingulate gyrus (BA32); and in the left middle temporal gyrus (BA21), spreading to the left superior temporal gyrus (BA22). Convergence of hyperactivation was reported in patients (n = 536) in the left medial frontal gyrus (BA9), spreading to the left superior frontal gyrus and the left middle frontal gyrus. Separate analysis of the mood disorders subgroup further highlighted convergence of hyperactivation in the insula and claustrum. The implications of the current findings are discussed within the context of the Research Domain Criteria (RDoC) framework of developing diagnostic systems that are more predictive of treatment outcomes.