In this 2-session functional MRI study, we investigated the neurocognitive mechanisms of counterconditioning (CC). We observed ventromedial prefrontal cortex (vmPFC) activation during regular extinction, but vmPFC deactivation and nucleus accumbens activation during CC (MRI). Physiological threat responses returned in the regular extinction but not the CC group (Pupil). Furthermore, threat-associated memories from the learning and CC phase were enhanced (Behavior). This collection contains the raw, pseudonomized data of all tasks. Processed data, the SPSS mask to replicate all but the fMRI analyses (Analyses.sav), and scripts to replicate the publication figures are available at https://osf.io/mvsq6. For all tasks, fMRI, skin conductance (SCR) and pupil dilation (Pupil) data are available. For the item memory test, behavioral data (Behavior) are available. In addition, valence and arousal rating data using self-assessment manikin scales are available.