A facile, safe, and environmentally friendly approach to the preparation of poly(β‐cyclodextrin‐co‐guanidinocitrate) (ZWβCDP) via polymerization of β‐cyclodextrin (β‐CD) in the presence of guanidinocitrate as a novel cross‐linker is reported. Novel zwitterionic guanidinocitrate cross‐linker is synthesized by in situ reaction of melted guanidine and citric acid during polymerization. The structure of achieved hydrogels is characterized by attenuated total reflection‐Fourier‐transform infrared (ATR‐FTIR), X‐ray photoelectron spectroscopy, thermogravimetric analysis, differential thermogravimetric, differential scanning calorimetry (DSC), differential of DSC, and X‐ray diffraction analyses and also by Kjeldahl and colorimetric methods for elemental analyses. The swelling ratio of the anionic β‐CD polymer (ANβCDP) and ZWβCDPs is determined in water and simulated physiological media. Subsequently, the hydrogels/ciprofloxacin (CFX, as a model antibiotic drug) complexes are prepared to improve the thermal stability of CFX and define potential pharmaceutical applications of hydrogels. Solid‐state characterization of hydrogels/CFX complexes is investigated by ATR‐FTIR and DSC. The in vitro release behavior of CFX from hydrogels is investigated at simulated physiological media, which exhibit initial burst and then slow drug release. The CFX release from ZWβCDP is slower than ANβCDP.