In the present work, the first manganese(II) heterodinuclear complex with enrofloxacin (Henro) has been synthesized and characterized using the following methods: elemental analysis, FT-IR, Raman, ultraviolet–visible (UV–Vis) spectroscopy, molar conductivity and single-crystal X-ray diffraction. In the complex structure, the deprotonated bidentate enrofloxacin ligands (Enrofloxacinate, Enro) are coordinated to manganese(II) via the pyridone oxygens and carboxylato oxygens. Sodium(I) is surrounded by carboxylate oxygens from three Enro ligands and oxygens from three water molecules. It should also be noted that, manganese(II) and sodium(I) have the distorted octahedral coordination geometry. Binuclear Na(I)⋯Mn(II) unit is linked by three carboxylate oxygens of Enro ligands. This crystal structure is the first example of a binuclear complex of sodium(I) and manganese(II) with carboxylate bridge. The antimicrobial activity of the complex was evaluated against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) strains by using broth microdilution, well diffusion, and growth inhibition methods. In all experiments, a higher antimicrobial activity of the complex was observed compared to the free ligand.