The strain of Bacillus sp. RD26, isolated from Phyllanthus amarus Schum. et Thonn. exhibited antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). In the current study, Bacillus sp. RD26 was identified as Bacillus amyloliquefaciens according to Cowan and Steel classification keys. The methanol extract (BRM) from Bacillus amyloliquefaciens RD26 was resistant to MRSA bacteria with an inhibition zone of 25 ± 0.57 mm. From total BRM, the high-efficient column chromatographic extraction was conducted with solvent system EA:Me (the ration of EA: Me were 100:0; 90:10; 80:20; 70:30; 60:40; and 0:100) to collect total of five fractions (BRM1 - BRM5). As the result, all fractions had antibacterial activity against MRSA. Among them, the fraction of BRM3 had the highest anti-MRSA ability with the zone of inhibition reached to 18 mm. Combining the method of column chromatographic extraction and thin-layer chromatographic extraction, the compound of BR04, pyrimidine-2,4-dion (Uracil), which had the anti-MRSA ability, was isolated. BR04 was identified to be resistant to many Gram-positive and Gram-negative bacteria such as MRSA, Bacillus cereus, Escherichia coli by evaluation of MIC. The values of MIC were 64 μg/mL, 128 μg/mL, and 512 μg/mL for MRSA, Bacillus cereus, and Escherichia coli, respectively. Additionally, BR04 had antioxidant activity at the concentration of 1800 μg/mL. In conclusion, the current study reported bioactive compounds from Bacillus amyloliquefaciens RD26 had the potential to be further applied against infectious microorganisms.