Semicarbazones and their transition metal complexes have been investigated as biologically active compounds. This study explores the synthesis, X-ray crystallographic structure, and characterization of a novel Co(III) complex cation with a pyridoxal-isothiosemicarbazone (PLITSC) ligand, [Co(PLITSC-2H)(NH3)3]+. The structure of the complex was further elucidated by the elemental analysis and spectroscopic techniques (IR and UV–VIS). Hirshfeld surface analysis was applied for the investigation of intermolecular interactions governing crystal structure. Optimization was performed at the B3LYP/6-31 + G(d,p)(H,C,N,O,S)/LanL2DZ(Co) level of theory without any geometrical constraints. The selected level of theory’s applicability was proven after comparing experimental and theoretical bond lengths and angles. The antibacterial activity of the complex towards E. coli and B. subtilis was determined and qualified as moderate compared to Streptomycin. The formation of free radical species in the presence of the complex was further verified in the fluorescence microscopy measurements. The molecular docking towards neural nitric-oxide synthase in the brain has shown that the complex structure and relative distribution of ligands were responsible for the binding to amino acids in the active pocket.