Background: Perceived purpose in life (PIL) is linked with many vital health outcomes, including Major Depressive Disorder (MDD). Methods: In this study, biomarkers associated with depression and PIL were investigated using Brain Network Activation (BNA) based quantitative electroencephalography (QEEG) and event-related potential (ERP) measures in a sample of individuals with MDD. Data were analyzed before and after a 36-session, Deep transcranial magnetic stimulation (TMS) program. Results: At baseline, the study observed that increased slow-frequency resting-state activity in the frontal and temporal regions correlated with higher levels of depression and reduced PIL. Additionally, a reduced P3b amplitude was found to predict elevated depressive symptoms. However, with the application of Deep TMS treatment notable improvements were observed in both depression (p < .001. d = 2.15) and PIL (p < .001, d = 1.59) levels. The treatment also successfully regulated resting-state QEEG (delta/beta) and ERP characteristics (P200 latency), bringing them closer to healthy levels. Conclusions: This attenuation of brain activity patterns relating to depression is encouraging as it suggests that effects were robust and are more likely to be sustained over time. This study represents the first exploration of the effects of Deep TMS on PIL and relevant QEEG and ERP biomarkers. The initial evidence suggests that Deep TMS holds promise in enhancing both PIL and neurophysiological health. Future investigations should continue exploring the utility of Deep TMS in targeting a wide range of neuropsychological and physical health conditions, leveraging objective biomarkers such as QEEG and ERP.