This study investigated the bioactive properties of Bacillus amyloliquefaciens RD26, an endophyte isolated from Phyllanthus amarus. The methanol extract of Bacillus sp. RD26 showed significant antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), with an inhibition zone of 25 ± 0.57 mm. The antibacterial compound, BR04, was isolated and identified as pyrimidine-2,4-dione (uracil), showing potent antimicrobial effects with minimum inhibitory concentrations (MICs) of 64 µg/mL against MRSA, 128 µg/mL against Bacillus cereus, and 512 µg/mL against Escherichia coli. In addition, BR04 showed antioxidant activity and scavenged up to 50% of DPPH free radicals at a concentration of 1800 μg/mL. These findings highlight the potential of BR04 as a bioactive compound for pharmaceutical and agricultural applications, particularly in combating infectious pathogens and providing a natural alternative to synthetic antioxidants.