The aim of the present study is to synthesize new metal complexes of 6-methyl-2-thiouracil and 6-propyl-2-thiouracil, elucidate their structures, and investigate their biological properties. All metal complexes were obtained after mixing water solutions of the corresponding metal salts and the ligand dissolved in DMSO and water solutions of NaOH in a metal-to-ligand ratio of 1:4:2. The structures of the new compounds are discussed based on melting point analysis (MP-AES) for Cu and Pd, UV-Vis, IR, ATR, 1H NMR, 13C NMR, and Raman spectroscopy. The interpretation of complex spectra is assisted by the data for 6-methyl-2-thiouracil and 6-propyl-2-thiouracil obtained from 1H-1H COSY, DEPT-135, HMBC and HMQC spectra. In addition, the antimicrobial activity of these complexes and the free ligands are assessed against both Gram-positive and Gram-negative bacteria, as well as yeasts. In general, the addition of metal ions improved the antimicrobial activity of both 6-methyl-2-thiouracil and 6-propyl-2-thiouracil. The Cu(II) complex with 6-methyl-2-thiouracil and the Pd(II) complex with 6-propyl-2-thiouracil exhibited the highest activity against the test microorganisms.