Chemotherapy can cause several long-term side effects that can affect cancer survivors' quality of life-, notably cognitive decline in response to select chemotherapeutic agents. Studies using both human patients and animal models have been employed to determine the regions of the brain that are subject to the most considerable changes, furthermore, elucidating possible molecular mechanisms of chemotherapy-induced cognitive impairment (CICI). However, the reason behind the differences in symptoms and duration of CICI between patients have yet to be identified. This study focused on understanding whether the systemic delivery of doxorubicin and cyclophosphamide (AC chemotherapeutics) causes any epigenetic factors to change in the female rat prefrontal cortex (PFC), possibly providing an insight into the variability of clinical manifestations of CICI. We evaluated DNA methylation levels and patterns in the PFC after AC-chemotherapy administration. We also demonstrated changes in histone deacetylase and acetyl transferase activity levels in the murine PFC in response to treatment. Despite no change in the global DNA methylation level, we found that several genes related to neuronal development and maintenance were differentially methylated in the promoter and exon regions in the rat PFC. Our study showed a significant increase in the expression of the de novo DNA methyl transferase DNMT3a compared to the control.