The bioavailability of ciprofloxacin (CIP) is known to decrease upon administration due to its complexation with iron present in the body. A possible way to prevent this complexation is by entrapping the drug in a carrier. In this study, Halloysite Nanotubes (HNT) post functionalization with 3-aminopropyltriethoxysilane (APTES) were used as ‘nanocarrier’ for the entrapment of CIP. The complexation studies between CIP and iron revealed 71% ± 1.2% decrease in drug's absorbance upon complexation. Further, the in vitro antibacterial studies also exhibited a reduction in the antibacterial property of CIP on complexation with iron. Pristine HNT exhibited no interaction with CIP and iron. But post functionalization, the nanotubes had a strong interaction with iron and removed 80% ± 0.9% of it from the solution. Drug loading studies using functionalized HNT (fHNT) presented a 70% ± 1.7% loading of CIP on it. The samples of HNT (before and after functionalization and after drug loading) were characterized with TEM, XRD, FTIR and DSC. The drug release studies exhibited a sustained release of CIP from drug loaded fHNT. Further, drug loaded fHNT (CIP-fHNT) removed iron from the iron-rich solution and released the loaded drug back into the solution.