Emotion regulation is an indispensable part of mental health and adaptive behavior. Research into emotion regulation processes has largely focused on the concurrent effects of volitional emotion regulation. However, there is scarce evidence considering post-regulatory effects with regard to neural mechanisms and emotional experiences. Therefore, we compared concurrent effects of cognitive emotion regulation with effects at different (immediate, short- and long-term) time intervals. In an fMRI study with N = 46 (N = 30 at re-exposure) young healthy adults, we compared neuronal responses to negative and neutral pictures while participants had to distance themselves from or to actively permit emotions in response to these pictures. We investigated the temporal dynamics of activation changes related to regulation in cognitive control brain networks as well as in the amygdala during stimulation (concurrent effects, timepoint 1) and post-stimulation (immediate, timepoint 2), as well as during re-exposure with the same pictures after short (10 minutes, timepoint 3) and long (1 week, timepoint 4) time intervals. At timepoint 1, negative pictures (versus neutral pictures) elicited a strong response in regions of affective processing, including the amygdala. Distancing (as compared to permit) led to a decrease of this response, and to an increase of activation in the right middle frontal and inferior parietal cortex. We observed an interaction effect of time (stimulation vs. post-stimulation) and regulation (distance vs. permit), indicating a partial reversal of regulation effects during the post-stimulation phase (timepoint 2). Similarly, after 10 minutes (timepoint 3) and after 1 week (timepoint 4), activation in the amygdala was higher during pictures that participants were previously instructed to distance from as compared to permit. These results show that the temporal dynamics are highly variable both within experimental trials and across brain regions. This can even take the form of paradoxical aftereffects at immediate and persistent effects at prolonged time scales.