By using the streptozotocin- (STZ-) induced cytotoxicity in β-TC3 cells as an assay model, a bioassay-guided fractionation study was employed to isolate and characterize the potential antidiabetic principles of roots of Prosopis farcta. A combination of open column chromatography on reverse-phase silica gel using a water-ethanol gradient (10 : 90 to 100 : 0) followed by HPLC-based fractionation led to an active compound that appears to be composed of carbohydrate/sugar. When cell viability under STZ was reduced to 49.8 ± 4% (mean ± SD), treatment with the active compound at the concentration of 0.5 mg/mL either as a coadministration or a pretreatment improved the viability to 93 ± 1.9% and 91.5 ± 7%, respectively. The reduction in the mitochondrial membrane potential by STZ (47.34 ± 8.9% of control) was similarly recovered to 84.5 ± 4.3 (coadministration) and 88 ± 5.5% (pretreatment) by the active fraction. The bioassay-guided fractionation, β-cell protective effect, and increased glucose consumption (up to 1.49-fold increase) in hepatocytes by the extracts and active fraction are also discussed.