Emotion regulation by means of cognitive reappraisal has been widely studied with functional magnetic resonance imaging (fMRI). To date, several meta-analyses of studies using cognitive reappraisal tasks in healthy volunteers have been carried out, but no meta-analyses have yet been performed on the fMRI data of clinical populations with identified alterations in emotion regulation capacity. We provide a comprehensive meta-analysis of cognitive reappraisal fMRI studies in populations of patients with mood or anxiety disorders, yielding a pooled sample of 247 patients and 262 controls from thirteen independent studies. As a distinguishing feature of this meta-analysis, original statistical brain maps were obtained from six of these studies. Our primary results demonstrated that patients with mood and anxiety disorders recruited the regulatory fronto-parietal network involved in cognitive reappraisal to a lesser extent in comparison to healthy controls. Conversely, they presented increased activation in regions that may be associated with the emotional experience (i.e., insula, cerebellum, precentral and inferior occipital gyri) and in regions whose activation may be the consequence of compensatory mechanisms (i.e., supramarginal gyri and superior parietal lobule). Moreover, activations in the left ventrolateral prefrontal cortex and the left superior temporal gyrus were associated with reinterpretation emotion regulation strategies, whereas medial frontal and parietal activations were associated with the deployment of distancing strategies. The regions revealed by this meta-analysis conform to a pattern of dysfunctional brain activation during cognitive reappraisal common to mood and anxiety disorders. As such, this neural pattern may reflect a transdiagnostic feature of these disorders.