In an effort to understand the factors that contribute to heterogeneity in outcomes often associated with mTBI in youth, this study examined the role of premorbid differences in cognitive reserve on post-concussive symptoms (PCS), molecular markers, and treatment response. Male and female rats matured in one of three environmental conditions (Stress, Enrichment, Control), received a mTBI in adolescence, and were randomized to melatonin or placebo treatment. All animals underwent a behavioural test battery designed to examine PCS. Using prefrontal cortex and hippocampus tissue, expression of 9 genes was assessed in an effort to determine how the brain's epigenome was influenced by cognitive reserve, mTBI, and melatonin. Enrichment increased cognitive reserve (CR) and prevented lingering symptoms. Conversely, stress was associated with progressive worsening and manifestation of PCS in the longer-term. Melatonin was able to restore baseline function for control and enriched animals, but was ineffective for the stress condition. Epigenetic change in the prefrontal cortex was largely driven by the injury, while gene expression changes in the hippocampus were dependent upon cognitive reserve. The occurrence and severity of PCS is dependent upon a complex and multifaceted array of factors that modify behavioural and epigenetic responses to mTBI and its treatment.