We sought to identify baseline (pre-treatment) neural markers associated with treatment response in major depressive disorder (MDD), specific to treatment type, Cognitive Behavioral Therapy (CBT) or pharmacotherapy (selective serotonin reuptake inhibitors; SSRI). We conducted a meta-analysis of functional magnetic resonance imaging (fMRI) studies to identify neural prognostic indicators of response to CBT or SSRI. To verify the regions derived from literature, the meta-analytic regions were used to predict clinical change in a verification sample of participants with MDD who received either CBT (n = 60) or an SSRI (n = 19) as part of prior clinical trials. The meta-analysis consisted of 21 fMRI studies that used emotion-related tasks. It yielded prognostic regions of the perigenual (meta pgACC) and subgenual anterior cingulate cortex (meta sgACC), associated with SSRI and CBT response, respectively. When applying the meta-analytic regions to predict treatment response in the verification sample, reactivity of the meta pgACC was prognostic for SSRI response, yet the effect direction was opposite of most prior studies. Meta sgACC reactivity failed to be prognostic for CBT response. Results confirm the prognostic potential of neural reactivity of ACC subregions in MDD but further research is necessary for clinical translation.