Papaya (Carica papaya L.) is a herbaceous plant belonging to the family Caricaceae in the order Brassicales. The shape of papaya fruit was linked to sex, and the fruit of female plants is round, whereas that of hermaphrodites is pyriform. Although fruit shape preferences vary by region, differences in their functionalities have not been investigated. Since unripe fruit, also called green papaya, is known for its nutritional and therapeutic benefits, we performed a metabolome analysis of unripe papaya using liquid chromatography coupled with quadrupole/time of flight mass spectrometry. We first focused on capraine derivatives, major piperidine alkaloids, and bioactive compounds with significant antiplasmodial activity. Interestingly, carpaine derivatives tended to be altered in the peel and pulp but not in the seed. Multivariate analyses indicated little difference or minor differences to the extent that they can be caused by individual differences in metabolite profiling between the two sexes. Conversely, total polyphenol content and proteolytic activity were also investigated, but there were no differences between females and hermaphrodites for total polyphenol content and proteolytic activity. In conclusion, the metabolome and major functionalities were similar between hermaphrodites and female unripe fruit. However, it would be worth considering the sex of the material fruit, especially when focusing on the functional properties of carpaine derivatives.