This study investigates the eco-friendly extraction of heat sensitive bioactive compounds from Parthenium hysterophorus L. using supercritical carbon dioxide (SC-CO₂) and compares its efficacy with Soxhlet extraction (SE) via gas chromatography–mass spectrometry (GC-MS) analysis. The SC-CO₂ extraction was performed at 3 each temperature (40 °C, 50 °C and 60 °C) and pressures (100, 150 and 200 bar) to evaluate extraction yield (EY), total phenolic content (TPC) and antioxidant activity (% AO). A 3×3 two-factorial dataset was analysed using a two-factor interaction (2FI) model and its statistical significance was confirmed through ANOVA (R² and F-values at 99 % confidence level). Numerical optimisation using a desirability function identified 60 °C and 200 bar as the optimal parameters, achieving the highest desirability score of 0.982. At these optimised conditions, SC-CO₂ yielded 13.14 g of extract, significantly higher than Soxhlet (6.44 g) due to improved mass transfer resulting from cell wall disruption and reduced intermolecular forces. The SC-CO₂ extraction also achieved a significantly higher TPC (74.31 mg GAE g-1) compared to Soxhlet (54.65 mg mg GAE g-1), which indicates superior antioxidant activity, peaking at 91.44 %. The GC-MS profiling of SC-CO₂ extracts identified twelve bioactive compounds, including novel constituents such as Phenol, 2,4-bis(1,1-dimethylethyl)- and Hexatriacontane. Overall, SC-CO₂ extraction provides a clean, efficient and value-added approach for converting invasive plant biomass into high-value herbal therapeutics.