Sex differences in brain function and disease are influenced by gonadal hormones, which regulate protein expression in the prefrontal cortex (PFC) essential for cognition and emotional regulation. Clinical trials of menopausal hormone therapies for neurodegenerative diseases have resulted in conflicting therapeutic outcomes dependent on the timing of drug introduction after menopause. Tibolone, a synthetic steroid with estrogenic, progestogenic, and androgenic properties, shows promise for neuroprotection but its molecular mechanisms under different hormonal states remain unknown. We hypothesized that Tibolone efficacy on the prefrontal cortex proteome is dependent on gonads in male and female mice. Through proteomic analysis, we employed dimensionality reduction techniques to explore sex-specific and shared proteomic responses to gonadal hormone deprivation and Tibolone treatment. Our findings reveal that gonadectomy induces a functional convergence of the PFC proteome in both male and female mice, erasing many sex-specific differences in pathways associated with calcium regulation, cytoskeletal function, and mitochondrial metabolism. Tibolone induced distinct sex-specific proteomic trajectories, while in gonadectomized animals, responses converged toward shared molecular pathways. Functional enrichment analysis identified differential regulation of synaptic plasticity, neurotransmitter signalling, and cellular stress response pathways. These results provide novel insights into the critical window hypothesis of hormone therapy, demonstrating that the underlying neurosteroid environment alters hormone therapy efficacy. Our findings suggest that optimal neuroprotective strategies will require sex-specific and timing-specific approaches, establishing a molecular framework for precision hormone therapy in neurodegeneration.