Considerable research has been carried out on medicinal plants for bioactive compounds except bacterial endophytes of plants which could serve as good source of novel antibiotic agents. This study was aimed to determine the antibacterial activity of secondary metabolites of endophytic bacterial isolates of Carica papaya against Klebsiella species and Staphylococcus aureus. Clinical isolates; Klebsiella species and Staphylococcus aureus were confirmed using morphological and biochemical standards. Bacterial endophytes were also cultured, isolated and identified using morphological and biochemical tests and the endophytes isolated designated as PL, PS, PR1 and PR2 which were all Gram negative rod. The bacterial endophyte PL1 was presumed to be Flavobacterium species, Enterobacter species for PS and PR1 while Proteus species for PR2. The endophytes were screened for bioactive secondary metabolites with antibacterial activity using ethyl acetate extract and agar well-diffusion method. Secondary metabolites from PS and PR2 showed strong antibacterial activity against Klebsiella species only with zones of inhibition of 18mm and 22mm respectively while that of PL and PR1 showed no zones of inhibition against both clinical isolates. Ethyl acetate extract of secondary metabolite was then subjected to phytochemical screening where flavonoid and phenol were detected and confirmed using Thin Layer chromatography (TLC) plates developed in ethyl acetate and Methanol chamber (8:2). Flavonoid and Phenol are known to possess antibacterial activities and as such could be responsible for the antibacterial activity against the clinical isolates. Therefore, bacterial endophytes from Carica papaya root could serve as a good source for the development of therapeutic drugs.