Near infrared reflectance spectroscopy (NIRS) coupled with a geometric study was used to estimate the oil content and fatty acid composition of Pongamia pinnata seed powder and seed oil. Sixty seed powders and seed oils from various sources of P. pinnata in southern Thailand were scanned by NIRS. All samples were analysed for oil content by hexane extraction and fatty acid composition by gas chromatography. Calibration equations were developed for oil content and individual fatty acids (palmitic acid C16:0, stearic acid C18:0, oleic acid C18:1, linoleic acid C18:2, and behenic acid C22:0). The results showed that NIRS was a reliable and accurate technique to estimate oil content from seed powder, as well as the concentrations of oleic, behenic, and linoleic acid in seed oil. Screening by NIRS of P. pinnata seed powders and seed oils represents a rapid, simple, and cost-effective alternative method that may be of great utility for analysing a large number of seed samples for tree breeding and plantations for the biofuel industry.