Compounds synthesized from carbohydrate substrates have yielded promising lead molecules for pharmaceutical developments, as many are approved for the clinical management of a wide range of diseases. Among them, thiourea moieties are the gold mines of antibacterial molecules. In view of the lack and need for new antibiotics, a series of 16 D-fructose-based thiourea compounds were synthesized from asymmetric aldol reaction and isopropylidenation. The new compounds were established from nuclear magnetic resonance, Fourier-transform infrared, and electrospray ionization mass spectrometry. Using disk diffusion assay for antibiotic susceptibility, four of the novel compounds were found to have concentration-dependent antibacterial activities. The addition of trifluoromethyl groups at the meta-position on the phenyl ring of the thioureas appeared to promote bacterial inhibitory action. Thiourea 2a exhibited the most potent activity against the Gram-negative species, Klebsiella pneumoniae, Escherichia coli, and Salmonella typhi, as well as the Gram-positive species, Micrococcus luteus; but not against all bacteria tested. Thiourea 2b and 3a had lower efficacy but showed better broad-spectrum activity against most bacteria tested. Thiourea 3b displayed species-specific activity only against K. pneumoniae and S. typhi. Our findings show the benefits and prospects of synthesizing new carbohydrate compounds for therapeutic medication.