Selenium is an essential trace mineral for various functions in the body and is known as an antioxidant. To evaluate the anti-obesity effect of sodium selenite (SS), we examined the expressions of epigenetic regulatory enzymes and the anti-adipogenic and lipogenic effects of SS in MDI-induced 3T3-L1 preadipocytes. SS significantly inhibited protein arginine methyltransferase 5 (PRMT5) and histone acetyltransferase (HAT) activity compared with a control, epigallocatechine gallate. SS also attenuated lipid accumulation and triglyceride formation in 3T3-L1 adipocytes. In addition, SS decreased the protein and mRNA levels of adipogenic transcription factors such as peroxisome proliferator-activated receptor gamma, CCAAT/enhaner binding protein alpha. SS effectively suppressed the mRNA expressions of the fatty acid synthase and ATP citrate lyase known as the lipogenic markers and the P300/CBP-associated factor known as an epigenetic regulatory marker in 3T3-L1 adipocytes. Consequently, the anti-obesity effect of SS is likely attributed to the inhibition of PRMT5 and HAT activity.