Due to their high entrapment efficiency, anodized titanium nanotubes (TiO2-NTs) are considered effective reservoirs for loading/releasing strong antibiotics whose systemic administration is associated with diverse and severe side-effects. In this study, TiO2-NTs were synthesized by anodic oxidation of titanium foils, and the effects of electrolyte percentage and viscosity on their dimensions were evaluated. It was found that as the water content increased from 15 to 30%, the wall thickness, length, and inner diameter of the NTs increase from 5.9 to 15.8 nm, 1.56 to 3.21 µm, and 59 to 84 nm, respectively. Ciprofloxacin, a highly potent antibiotic, was loaded into TiO2-NTs with a high encapsulation efficiency of 93%, followed by coating with different chitosan layers to achieve a sustained release profile. The prepared formulations were characterized by various techniques, such as scanning electron microscopy, differential scanning calorimetry, and contact measurement. In vitro release studies showed that the higher the chitosan layer count, the more sustained the release. Evaluation of antimicrobial activity of the formulation against two endodontic species from Peptostreptococcus and Fusobacterium revealed minimum inhibitory concentrations (MICs) of 1 µg/mL for the former and the latter. To summarize, this study demonstrated that TiO2-NTs are promising reservoirs for drug loading, and that the chitosan coating provides not only a sustained release profile, but also a synergistic antibacterial effect.