Depressive rumination is considered a prominent risk factor for the occurrence, severity, and duration of depressive episodes. A variety of treatment options have been developed to treat depressive rumination of which mindfulness based programs are especially promising. In the current study, we investigated the neural underpinnings of a short mindfulness intervention and mindful emotion regulation in high and low trait ruminators in an ecologically valid environment using functional near-infrared spectroscopy (fNIRS). Participants were randomly assigned to a mindfulness instruction (MT) group or an instructed thinking (IT) group. Participants in the MT group were trained to either focus their attention mindfully on their breath or their emotions, while the IT group focused their attention on the past or future. Afterwards, all participants underwent an emotion regulation paradigm in which they either watched negative or neutral movie clips. During both paradigms cortical hemodynamic changes were assessed by means of fNIRS. Participants in the MT group showed lower activity in the cognitive control network (CCN) during the focus on breath condition in comparison to the focus on emotion condition. Additionally, oxygenated hemoglobin in the MT group tended to be lower than in the IT group. Further, self-reports of emotional distress during the instruction paradigm were reduced in the MT group. During the emotion regulation paradigm, we observed reduced emotional reactivity in terms of emotional distress and avoidance in the MT group in comparison to the IT group. Furthermore, on a neural level, we observed higher CCN activity in the MT group in comparison to the IT group. We did not find any effect of rumination, neither on the intervention nor on the emotion regulation task. The results of this pilot study are discussed in light of the present literature on the neural correlates of mindfulness based interventions in rumination and emphasize the use of fNIRS to track neural changes in situ over the course of therapy.