Urea inclusion is a fractionation technique based on the selective formation of crystalline complexes between urea and fatty acids or their esters. In this study, crude palm oil (CPO) was first converted into fatty acid ethyl esters (FAEEs) through transesterification. The resulting FAEEs were then mixed with urea dissolved in ethanol, followed by solvent evaporation and crystallization to obtain solid and liquid fractions. This study aimed to evaluate the effect of urea concentration on the distribution of β-carotene and the concentrations of saturated and unsaturated FAEEs in both fractions. The results showed that CPO had a high free fatty acid (FFA) content of 3.24 ± 0.13%, which decreased by 46% following neutralization. Transesterification converted CPO into FAEEs with a yield of 87.79% and increased the carotenoid content by 1.67-fold. Furthermore, the urea inclusion of FAEE increased the solid fraction from 29.49% to 92.95%, and it decreased the liquid fraction from 70.51% to 7.05% (p < 0.05) significantly, with increasing the FAEE-to-urea ratio from 1:1 to 1:5. Besides, increasing urea ratios from 1:1 to 1:5 significantly enriched carotenoids in the liquid fraction from 772 to 2,308 ppm, while it remained low in the solid fraction. This indicates that β-carotene is not effectively entrapped in the urea crystals and mostly remains in the liquid fraction. Carotenoid recovery in the liquid fraction decreased from 67.86% to 21.08, while carotenoid recovery in the solid fraction increased from 4.01 to 40.28% with increasing urea ratios. Palmitic acid was the predominant saturated fatty acid in CPO, whereas oleic acid was the major unsaturated fatty acid. Overall, unsaturated fatty acids accounted for 55.26% of the total fatty acid content, exceeding the proportion of saturated fatty acids after the inclusion. Thus, urea inclusion increases carotenoid content in the liquid fraction and alters fatty acid composition. Further research can be conducted to improve FAEE yield and carotenoid recovery such as adjusting the amount of urea. This research could be useful for development of CPO derivative product such as carotene and biodiesel.