The success rate of aquaculture is highly influenced by several factors, including optimum water quality, feed management, and microorganism control. Several microorganisms interfere with the quality of media and fish culture, i.e., fish growth. Aeromonas and Vibrio are the main pathogenic bacteria that disrupt fish growth and cause mortality. Sidr leaf (Ziziphus spina-christi) extract contains phytochemicals that have antibacterial properties. This study aimed to identify the phytochemical components and analyze the effect of Sidr leaf extract on the growth of aquaculture-based pathogenic bacteria. Sidr leaf extract was obtained using ethanol and tested via phytochemical analysis, chemical analysis, prediction of activity spectra for substances (PASS) examination, and inhibition capability against Aeromonas hydrophila, Aeromonas caviae, Aeromonas sobria, Pseudomonas putida, Pseudomonas aeruginosa, Streptococcus agalactiae, Vibrio vulnificus, Vibrio harveyi, Vibrio parahaemolyticus, and Vibrio alginolyticus. The results showed that Sidr leaf extract contained phytochemicals, namely, flavonoids, alkaloids, saponins, tannins, and steroids. Gas chromatography-mass spectrometry analyses showed that the Sidr leaf extract contained 30 compounds with antiseborrheic effects. PASS analysis demonstrated that 15 compounds (64.51% level) have potential as antibacterial, with a probability activity value of more than 0.300. The inhibition test showed that the Sidr leaf extract exhibited moderate-to-strong inhibition against pathogenic bacterial growth, except for V. vulnificus, for which it produced a weak inhibition. The results indicate that Sidr leaf extract can be used as a natural herb to control bacterial pathogens in fish cultivation.