Chitosan has become an established platform biopolymer with applications in biomedical engineering, nanomedicine, and the development of new materials with improved solubility, antimicrobial activity, and low toxicity. In this study, a series of chitosan derivatives were synthesized by conjugating various perfluorocarbon chains to chitosan via Schiff base formation or nucleophilic substitution, followed by quaternization with glycidyl trimethylammonium chloride to confer non-pH-dependent permanent positive charges. Synthesized fluorinated N-(2-hydroxypropyl)-3-trimethylammonium chitosan chloride polymers were characterized and investigated for their antibacterial efficacies against multidrug-resistant bacteria including clinical isolates. The polymers showed activity against both Gram-positive and Gram-negative bacteria (MIC = 64-512 μg/mL) but with greater potency against the former. They displayed rapid bactericidal properties, based on the MBC/MIC ratio, which were further confirmed by the time-kill kinetic assays. Given the properties presented here, fluorinated quaternary chitosan derivatives can serve as great candidates to be investigated as environmentally more benign, nontherapeutic antimicrobial agents that could serve as alternatives to the heavy reliance on antibiotics, which are currently in a very precarious state due to increasing occurrence of drug resistance.