Fusarium wilt caused by soil fungus like Fusarium oxysporum poses a significant threat to rice production around the world, including Pakistan and The Gambia. Conventional methods for managing such diseases are not sustainable. Therefore, the present study was carried out to evaluate the biocontrol potential of halotolerant plant growth-promoting rhizobacteria (PGPRs) against Fusarium oxysporum PF5. Out of 510 rhizobacteria isolates, 24 halotolerant isolates (11 from Pakistan and 13 from The Gambia) were selected to evaluate their potential against the growth of selected fungus. Dual cultures in vitro showed that isolate 6 and 11 from Pakistan and isolate B and G from The Gambia, inhibited the growth of fungi by 70%. These isolates also showed the production of hydrogen cyanide (HCN) (52 µg/mL) and glucanase (4 µg/mL). In addition, intense production of hydrolytic enzymes protease (70 µg/mL) and chitinase (4 µg/mL) was recorded by isolates 4 and 9 respectively. Scanning electron microscopy graphs evidenced a significant ultrastructural damaged and a severe hyphal breakdown by the bacterial isolates (6, 11 and B, G) in Fusarium co-cultures as compared to the control fungal culture. The GC-MS metabolomics highlighted the presence of key bioactive compounds such as oleic acid, imidazol [1,2-a] pyridine. Therefore, it can be concluded that the selected isolates can be considered as a promising candidate as a biocontrol agent against Fusarium wilt in rice on the basis of strong antifungal activity, hydrolytic enzymes and bioactive metabolites production as well as structural damage to Fusarium hyphae. The future work will focus on controlled pot experiment and then field application for practical implication of the selected isolates.