Opioid use disorder (OUD) is a neuropsychological disease that causes immense distress to individuals and the society. Despite the abundant clinical and preclinical studies demonstrating substantial individual differences in OUD vulnerability, the neurobiological mechanisms underlying such individual variability in OUD vulnerability remain unclear, hindering the progress in the development of more effective therapeutics. To address this question, we investigated the transcriptome (RNA-seq) and genome-wide chromatin accessibility (ATAC-seq) in the medial prefrontal cortex (mPFC) of male and female rats given morphine and exhibiting differential vulnerability to OUD as measured in behavioral paradigms capturing different phases of the disorder: Withdrawal-Induced Anhedonia (WIA), Demand, and Reinstatement. Ingenuity Pathway Analysis (IPA) of RNA-seq revealed greater changes in canonical pathways in Resilient (vs. Saline) rats in comparison to Vulnerable (vs. Saline) rats across 3 paradigms, suggesting brain adaptations that might contribute to resilience to OUD. Weighted Gene Co-Expression Network Analysis and IPA analyses suggested an involvement of myelination and oligodendrocyte processes, and neuroinflammation responses in the vulnerability associated with WIA and Demand paradigm, respectively. HOMER motif analysis of ATAC-seq showed changes in accessibility to a small set of transcription factor (TF) binding sites, some that were shared across the 3 paradigms and others that were unique to each. In conclusion, we have identified changes in biological pathways, TFs, and their binding motifs that vary with paradigm and disease vulnerability. These findings point to the involvement of distinct transcriptional and epigenetic mechanisms in response to opioid exposure, vulnerability to OUD, and different stages of the disorder.