Objectives: Carica papaya Linn. a member of the Caricaceae family, is a tropical fruit, rich in various secondary metabolites owing to its antioxidant, anti-inflammatory, anti-diabetic, and antihelmintic properties. The study was carried out to investigate the metabolic profiling and free radical scavenging compounds in C. papaya fruit's pulp, peel and seeds through thin-layer chromatography-mass spectrometry (TLC-MS) bioautography. Methodology: Aqueous, hydroalcoholic and alcoholic extracts of fruit pulp and peel were prepared along with the hydroalcoholic and hexane extract of seeds. These were subjected to total phenol, flavonoid and free radical scavenging estimation. Qualitative and quantitative high-performance thin-layer chromatography analysis of the best extracts was performed followed by TLC-MS bio autography assay for the detection of free radical scavenging compounds. Results: C. papaya peel was noted to contain the highest phenol and flavonoid content, but the seeds showed better free radical scavenging activity. The hydroalcoholic extracts of pulp, peel, and seeds examined through TLC-bioautography showed the presence of chlorogenic acid, ellagic acid, quercetin, β-sitosterol, linoleic acid, and iso-oleic acid as potent free radical scavenging compounds. Liquid chromatography-mass spectrometry analysis showed the presence of β-carotene, lycopene, and β-cryptoxanthin in pulp and peel along with other carotenoids and benzyl isothiocyanate, linoleic acid, oleic acid, and methyl palmitate were the major compounds detected in seeds through gas chromatography-mass spectrometry analysis. Conclusion: This study has revealed that C. papaya fruit and seeds possess potent free radical scavenging compounds. Seeds which make up the waste material may be utilized in cosmetic industries as they signify rich antioxidants.