Microbial secondary metabolites are biologically active natural compounds that exhibit a broad range of antimicrobial properties. Investigating rhizobacterial resources could lead to the development of new antimicrobial compounds to enhance biocontrol agents. In this study, six Bacillus isolates (KSAS15-KSAS20) were isolated from the potato rhizosphere and screened in vitro for their ability to inhibit the growth of the phytopathogenic fungus, Sclerotium bataticola. The antifungal efficacy of the bacterial strains was assessed in vitro using a dual culture antagonism assay. The results demonstrated that strain KSAS17 had the most significant antagonistic activity, achieving a growth inhibition rate of 31.4%. The sequencing and analysis of the 16S rRNA gene identified the bacterial isolates as Bacillus licheniformis (KSAS15, KSAS16, and KSAR19), Bacillus cereus (KSAS17 and KSAR18), and Lysinibacillus fusiformis (KSAR20). Gas chromatography-mass spectrometry analysis of ethyl-acetate extract of the bacterial culture filtrate revealed that the compound most likely responsible for the effects in strain KSAS17 is pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl). Furthermore, significant bioactive aliphatic and aromatic compounds were identified, including oleic acid, hexadecanoic acid, 1-tetradecanol, heptadecanoic acid, 5-fluoro-2,2-dimethylchroman-4-one, pentadecanoic acid, 3′,8,8′-trimethoxy-3-piperidyl-2,2′-binaphthalene-1,1′,4,4′-tetrone, and phthalic acid derivatives. These findings indicate that the secondary metabolites of the rhizobacteria B. cereus strain KSAS17 exhibit antifungal properties and may be effectively employed as a biocontrol agent for managing fungal diseases.