The capacity of palm oil production is directly affected by the ripeness of the fresh fruit bunches (FFB) upon harvesting. Conventional harvesting standards rely on rigid harvesting scheduling as well as the number of fruitlets that have loosened from the bunch. Harvesting is usually done every 10 to 14 days, and an FFB is deemed ready to be harvested if there are around 5 to 10 empty sockets on the fruit bunch. Technology aided by imaging techniques relies heavily on the color of the fruit bunch, which is highly dependent on the surrounding light intensities. In this study, Raman spectroscopy is used for ripeness classification of oil palm fruits, based on the molecular assignments extracted from the Raman bands between 1240 cm−1 and 1360 cm−1. The Raman spectra of 52 oil palm fruit samples which contain the fingerprints of different organic compounds were collected. Signal processing was applied to perform baseline correction and to reduce background noises. Characteristic data of the organic compounds were extracted through deconvolution and curve fitting processes. Subsequently, a correlation study between organic compounds was developed and eight hidden Raman peaks including protein, beta carotene, carotene, lipid, guanine/cytosine, chlorophyll-a, and tryptophan were successfully located. Through ANOVA statistical analysis, a total of six peak intensities from proteins through Amide III (β-sheet), beta-carotene, carotene, lipid, guanine/cytosine, and carotene and one peak location from lipid were found to be significant. An automated oil palm fruit ripeness classification system deployed with artificial neural network (ANN) using the seven signification features showed an overall performance of 97.9% accuracy. An efficient and accurate ripeness classification model which uses seven significant Raman peak features from the correlation analysis between organic compounds was successfully developed.