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The ‘Philippine Lono Tall’ (PLNT) is a variant of the more common ‘Philippine Laguna Tall’ (LAGT), which produces fruits with soft endosperm and reported higher fat content. To understand patterns of fatty acid (FA) and oil accumulation in LAGT and PLNT fruits, transcriptomes of 6–7 month-old endosperm samples were analyzed by RNA-Seq. Quantitative PCR was performed to analyze the differential expression of selected genes related to oil biosynthesis. Further, oil samples from the PLNT endosperm were analyzed to determine their FA composition across developmental stages. A total of 416,488 contigs were de novo assembled, including 15,497 (14,356 upregulated and 1,141 downregulated) differentially expressed contigs. Several putative unigenes related to cell membrane and wall biogenesis, endosperm development, and oil biosynthesis and accumulation were identified among the assembled contigs. This first report of the complete ontogenetic FA profile revealed that medium chain fatty acids are the main components of oil from the PLNT endosperm. This pilot study is the first to suggest a molecular basis for the unique ‘Lono’ phenotype.