In a recent study, snake fruit seed (SFS) flour was found to enhance haemoglobin levels in a rat model of anemia. Still, it increases leucocyte number and its differential count. The purpose of this study was to fractionate SFS Pondoh and to analyze phytochemical compounds in SFS fractions. Simplicia of SFS was separated into lipid, water, and organic fractions using tetrahydrofuran, methanol and ethyl acetate reagents, and then dried using a vacuum evaporator. Chemical components in the SFS fractions were analyzed using gas chromatography-mass spectrophotometry (GC-MS). We got 77.8%, 16.5%, and 7.5% fractions of water, organic, and lipid. The water fraction contained 13 active compounds with 19 to 22 min retention time (RT). The organic fraction also had 13 active compounds with 19 to 29 min RT. The last lipid fraction contained 15 active compounds with 3 to 25 min RT. In conclusion, SFS Pondoh generates the highest water fraction, followed by organic and lipid fractions.