<b><i>Introduction:</i></b> Currently, major depressive disorder (MDD) treatment plans are based on trial-and-error, and remission rates remain low. A strategy to replace trial-and-error and increase remission rates could be treatment stratification. We explored the heartbeat-evoked potential (HEP) as a biomarker for treatment stratification to either antidepressant medication or rTMS treatment. <b><i>Methods:</i></b> Two datasets were analyzed: (1) the International Study to Predict Optimized Treatment in Depression (iSPOT-D; <i>n</i> = 1,008 MDD patients, randomized to escitalopram, sertraline, or venlafaxine, and <i>n</i> = 336 healthy controls) and (2) a multi-site, open-label rTMS study (<i>n</i> = 196). The primary outcome measure was remission. Cardiac field artifacts were removed from the baseline EEG using independent component analysis (ICA). The HEP-peak was detected in a bandwidth of 20 ms around 8 ms and 270 ms (N8, N270) after the R-peak of the electrocardiogram signal. Differences between remitters and non-remitters were statistically assessed by repeated-measures ANOVAs for electrodes Fp1, Cz, and Oz. <b><i>Results:</i></b> In the venlafaxine subgroup, remitters showed a lower HEP around the N8 peak than non-remitters on electrode site Cz (<i>p</i> = 0.004; <i>d</i> = 0.497). The rTMS group showed a non-significant difference in the opposite direction (<i>d</i> = −0.051). Retrospective stratification to one of the treatments based on the HEP resulted in enhanced treatment outcome prediction for venlafaxine (+22.98%) and rTMS (+10.66%). <b><i>Conclusion:</i></b> These data suggest that the HEP could be used as a stratification biomarker between venlafaxine and rTMS; however, future out-of-sample replication is warranted.