The biological activity of acylthiourea compounds, which interact with biological systems due to their molecular structure and redox properties, is generally enhanced when converted to metal complexes. A novel series of five complexes with the formula of Na[ML2(N3)X] [M = Co(II) (1), Ni(II) (2), Cu(II) (3)] and K[ML2(SCN)] [M = Ni(II) (4), Cu(II) (5)] were synthesized using N-furfuryl-N’-benzoylthiourea (HL) with the aim of developing potential antibacterial reagents. The structure of the complexes was elucidated using elemental analysis, IR spectroscopy, thermal analysis, as well as molar conductance, and magnetic measurements. The results indicated that the N-furfuryl-N′-benzoylthiourea ligand behaves as a monobasic bidentate SO ligand. The antibacterial activity of the complexes was evaluated against Gram (+) and Gram (−) bacteria. The copper(II) complexes showed the highest antibacterial activity. Quantum chemical calculations of the complexes were performed at the DFT/B3LYP level of theory using the LANL2DZ basis set, which includes the effective core potentials for metal atoms, and the 6-311G(d,p) basis set for non-metal atoms. The geometric parameters, molecular electrostatic potential diagrams, total density of states and frontier molecular orbitals of each complex were calculated. Molecular docking simulation demonstrated the interactions of the compounds with two selected enzymes, β-ketoacyl-ACP synthase III, and lipoteichoic acid synthase, key enzymes for bacterial survival. Based on the binding energies, copper(II) complex had the best antibacterial activity. The best binding energy was between complex 5 and 1HNJ with an energy value of −9.2 kcal/mol. Molecular dynamics simulations confirmed the stability of the Complex 5-1HNJ couple under physiological conditions.