Background/Objectives: Fluorothiazinone (FT), a small molecule of the 2,4-disubstituted-4H-[1,3,4]-thiadiazine-5-one class, is known to inhibit the type III secretion system (T3SS) in Gram-negative bacteria and has shown therapeutic potential in animal models and clinical trials. Given the evolutionary relationship between the T3SS and the bacterial flagellar apparatus, this study aimed to investigate the effects of FT on bacterial motility and flagellum assembly. Methods: Motility was assessed in Pseudomonas aeruginosa, Proteus mirabilis, pathogenic Escherichia coli, and Listeria monocytogenes using a semisolid agar assay and a microfluidic motility system. The mechanism of FT’s action was further examined through time-course analysis, Western blotting of surface flagella proteins, and transmission electron microscopy (TEM). Results: FT inhibited motility of P. aeruginosa, P. mirabilis, and E. coli in a dose-dependent manner, while L. monocytogenes motility remained unaffected. The inhibitory effect was not immediate but delayed 2–3 h post FT addition. Western blotting revealed the absence of surface flagella in EHEC grown with FT, and TEM confirmed structural disruption of flagella in P. mirabilis. Conclusions: FT selectively inhibits flagellum-based motility in Gram-negative bacteria. Obtained data suggested FT interference with flagellum biosynthesis rather than disruption of rotation. Motility inhibition can contribute to FT therapeutic effects on Gram-negative bacterial infections.