Background: Zanthoxylum rhetsa (Rutaceae) has many biological activities and is widespread in Bangladesh, China, Indonesia, Malaysia, and India. Methods: The total methanolic extract and different successive extracts with phytoconstituents-rich fractions were prepared from Zanthoxylum rhetsa fruit by the Soxhlet extraction method. Meanwhile, antibacterial activity was also assessed to identify the most active extracts/fraction against Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pyogenes. HR-LCMS was also performed for alkaloid-rich fraction and flavonoid-rich fractions. Results: The findings of antibacterial activity indicated that alkaloid-rich and flavonoid-rich fractions were active against all the investigated bacterial strains, and all extracts/fractions were most active against E. coli with a higher zone of inhibition. Conclusion: The phytoconstituents-rich fraction comprised of a number of alkaloids and flavonoids probably identified for the first time by HR-LCMS. Meanwhile, extracts/fractions also were revealed to have significant activity against E. coli, B. subtilis, P. aeruginosa, S. aureus, and S. pyogenes.