The present study was designed to check the ability of cyanogenic antagonistic bacterial endophytes to produce volatile organic compounds and enhance growth of sunflower under Sclerotinia sclerotiorum stress. Forty endophytic bacteria were isolated and screened for antagonism against Sclerotinia sclerotiorum. Out of 40 endophytes, two isolates SEB1 and SEB21exhibited fungal growth inhibition of 30.0 and 36.6%, respectively, in dual plate assay and 78.7 and 82%, respectively, in liquid media. Scanning electron microscopy showed rupturing, breakage and shrinkage of the fungal hyphae in the presence of the antagonistic bacterial strains. In addition, the bacterial strains also exhibited phosphate solubilization, and production of hydrogen cyanide, siderophores, auxins, ammonia, lipase and cellulases. The isolates were identified as Sphingobacterium solani SEB1 and Pseudomonas sp. SEB21 by 16S rRNA gene sequencing. GCMS analysis confirmed the presence of dimethyl-sulfone, phenol, 3-hexadecene, 2,4-ditertbutylphenol, 1-docosene, 1-octadecene, 2,4-dimethylphenylimino-4-nitrophenyl, nonylcyclopropane 1-nonadecene, octacosane, n-octadecanol, isopropyl myristate, 3-hexadecene, 7,9-di-tert-butyl-1-oxosiro-4,5-deca-6,9-diene, 3,5-bis (1,1-dimethylethyl)-phenol, isopropyl myristate, 7,9-ditert-butyl-1-oxospiro (4,5) deca-6,9-diene-2,8-dione, 1-tricosene and octacosanol as major volatile organic compounds produced by the bacterial strains. SEM analysis showed colonization of plant tissues by both the bacterial strains validating their endophytic nature. The bacterial treatments showed disease control up to 88.9% and significantly improved vigor index, plant growth, total phenol and chlorophyll content over the uninoculated control in sunflower grown under greenhouse conditions. The treatment SsSEB1+PspSEB21 in the presence of the fungal pathogen showed 1.41%, 0.47% and 6.8% N, P and K content in plants, respectively, which was the highest among all the treatments. Further field-level evaluations are recommended to validate the effectiveness of Sphingobacterium solani SEB1 and Pseudomonas sp. SEB21 as biological control agents. Sphingobacterium solani as a biocontrol agent and a plant growth-promoting endophyte is reported here for the first time.