Fujairah honey, collected from the mountainous regions of the United Arab Emirates, represents promising natural sources of functional food and pharmacological potential. This study aimed to characterise the functional food properties of crude Fujairah honey and to employ fractionation approaches to identify constituents with anticancer potential. Twenty Fujairah honey samples (Samar and Sidr) obtained from distinct locations of Fujairah Emirate were evaluated and compared with Manuka honey. The relationship between cytotoxicity, physicochemical properties, and underlying molecular mechanisms including antioxidant capacity, anti-inflammatory, and antimetastatic effects was investigated. Among the samples, Sample 6 (Samar honey derived from Acacia species) demonstrated selective cytotoxic activity following fractionation. While the crude honey promoted cell proliferation, its dichloromethane (DCM) fraction induced a 20% reduction in Michigan Cancer Foundation-7 (MCF-7) cell viability. Sample 6 DCM exhibits strong antioxidant activity (92.47% 2,2-diphenyl-1-picrylhydrazyl-hydrate radical scavenging), antimetastatic effects, and significant anti-inflammatory effects through Interleukin-6 (IL-6) downregulation (p < .0001) without excessive immune stimulation. Metabolomics profiling revealed elevated levels of fatty acids and monoacylglycerides, and succinic acid (with 28% enhanced cytotoxicity), supporting the unique activity of Samar (particularly Sample 6) honey. Driven by Fujairah’s arid climate and unique flora, Fujairah honey emerges as a promising source of novel pharmaceutical and
nutritional applications, offering distinctive anticancer and immunomodulatory properties.