Functional connectivity measures have become one of the most common biomarkers when correlating brain activity to task and resting states post treatment. Mindfulness based stress reduction (MBSR) and cognitive behavioral therapy (CBT) are two well established forms of therapies treating clinical populations worldwide today. Although there are several studies that have investigated the neural correlations of these therapy forms individually, no systematic review has compared them side by side, to identify potential similarities and differences in functional connectivity. This systematic review attempts to shed light on how functional connectivity is altered during resting state after completed treatment, by reviewing a total of 4 CBT and 4 MBSR studies containing 337 participants. The results point to possible differences in resting state functional connectivity (rsFC) concerning the insula and similarities involving the cingulate cortex and other parts of the DMN. The insula has been suggested to be involved in the creation of motivation and the integration of bodily sensations and feelings. Furthermore, emotional reactions to personally valued behaviors and the retrieving of episodic memories is associated with the function of the cingulate cortex. These changes in rsFC might relate to the theoretical underpinnings of CBT and MBSR. However, more compelling research needs to be conducted before drawing conclusions on how these therapeutic approaches can alter rsFC and improve psychological health among individuals suffering from clinical conditions.