In this study, some new 4,6-dimethoxy pyrimidine derivatives were synthesized. 2-Amino-4,6-dimethoxy-5-thiocyanatopyrimidine (2) was synthesized by a reaction of 2-amino-4,6-dimethoxypyrimidine with KSCN and was converted into 2-amino-5-(1H-tetrazol-5-ylthio)-4,6-dimethoxypyrimidine (4) by treatment with NaN3 in the presence of NH4Cl in DMF. Then, 1,5-disubstitute tetrazole compounds were obtained from 4 by the alkylation reaction. In addition, some 2-chloro-4,6-dimethoxy-5-substitute-pyrimidines were synthesized by the diazotization method. The structures of these compounds were established on the basis of IR, H-1 NMR, APT, and HRMS spectral data and were evaluated for antibacterial activities against various bacterial strains. The results showed that some of these compounds exhibited good antibacterial activity as that of standard antibiotics Penicillin, Ampicillin, and Erythromycin.