Increasing attention has been given to mango (Mangifera indica) fruits owing to their characteristic taste, and rich nutritional value. Mango kernels are typically discarded as a major waste product in mango industry, though of potential economic value. The present study aims to outline the first comparison of different mango kernel cvs. originated from different localities alongside Egypt, e.g., Sharqia, Suez, Ismailia, and Giza. Gas chromatography–mass spectroscopy (GC–MS) post silylation analysis revealed that sugars were the major class being detected at 3.5–290.9 µg/mg, with some kernels originating from Sharqia province being the richest amongst other cvs. In consistency with sugar results, sugar alcohols predominated in Sharqia cvs. at 1.3–38.1 µg/mg represented by ribitol, iditol, pinitol, and myo-inositol. No major variation was observed in the fatty acids profile either based on cv. type or localities, with butyl caprylate as a major component in most cvs. identified for the first time in mango. Regarding phenolics, Sedeeq cv. represented the highest level at 18.3 µg/mg and showing distinct variation among cvs. posing phenolics as better classification markers than sugars. Multivariate data analyses (MVA) confirmed that the premium cvs “Aweis and Fons” were less enriched in sugars, i.e., fructose, talose, and glucose compared to the other cvs. Moreover, MVA of Zabdeya cv. collected from three localities revealed clear segregation to be chemically distinct. Sharqia originated mango kernels were rich in sugars (e.g., glucose and fructose), whilst sarcosine esters predominated in other origins.