Papaya fruits have great nutritional and economical values. The ripening stage of papaya fruits at the time of harvesting massively impacts the quality and shelf-life of fruits. Volatile organic compounds (VOCs) emitting from the papaya fruits during the ripening process could be used as a real-time non-invasive biomarker to characterize the ripening stage. This paper reports identification of VOCs as non-invasive ripening biomarkers of papaya fruits based on solid-phase micro-extraction coupled with gas chromatography–mass spectrometry (GC–MS) analysis of VOCs emitted from the papaya fruit cv. ‘Red Lady’. Three ripening stages were studied, viz., green unripe (UR), yellowish-green intermediate ripe (IR), and yellow full ripe (FR). GC–MS analyses and the subsequent statistical studies identified a total of 35 VOCs. Partial Least Squares Discriminant Analysis (PLS-DA) of VOCs from the three ripening stages identified six biomarker VOCs, which can efficiently distinguish between ripening stages. Among the six ripening biomarkers, three VOCs (methyl hexanoate, 3-carene and longifolene) showed a remarkable correlation with the ripening-associated changes in the fruit nutritional profile. The biomarkers reported here could be used as a viable technology for non-invasive monitoring of ripening stages and the nutritional value of papaya fruits.