This data article describes the analysis of volatile compounds in susceptible and resistant chili variety via gas chromatography/mass spectrometry (GC-MS). The volatile compounds from two chili varieties which have different level of resistance to fruit fly infestation were captured by a solid-phase micro extraction method. The obtained extracts were then subjected to GC-MS for separation and identification of the compounds in three developmental stages (buds, flowers and fruits). The retention times and the detected compounds were identified as well as their relative peak areas. The data were provided in Supplementary 1 (Table 1) and Supplementary 2 (Table 2).