Chaulmoogra oil is found in the seeds of Carpotroche brasiliensis (Raddi) Endl. (syn. Mayna brasiliensis Raddi), an oil tree of the Achariaceae family and native to Brazil’s Atlantic Forest biome, which is considered the fifth most important biodiversity hotspot in the world. Its main constituents are cyclopentenic fatty acids. Chaulmoogra oil has economic potential because of its use in the cosmetics industry and as a drug with anti-tumor activity. The mechanisms related to the regulation of oil biosynthesis in C. brasiliensis seeds are not fully understood, especially from a tissue-specific perspective. In this study, we applied a de novo transcriptomic approach to investigate the transcripts involved in the lipid pathways of C. brasiliensis and to identify genes involved in lipid biosynthesis. Comparative analysis of gene orthology, expression analysis and visualization of metabolic lipid networks were performed, using data obtained from high-throughput sequencing (RNAseq) of 24 libraries of vegetative and reproductive tissues of C. brasiliensis. Approximately 10.4 million paired-end reads (Phred (Q) > 20) were generated and re-assembled into 107,744 unigenes, with an average length of 340 base pairs (bp). The analysis of transcripts from different tissues identified 1131 proteins involved in lipid metabolism and transport and 13 pathways involved in lipid biosynthesis, degradation, transport, lipid bodies, and lipid constituents of membranes. This is the first transcriptome study of C. brasiliensis, providing basic information for biotechnological applications of great use for the species, which will help understand chaulmoogra oil biosynthesis.