Clinical treatments of significant bone defects involve invasive procedures such as the application of auto- and allografts. These procedures present many limitations including the potential for infection and rejection. There is therefore a need to develop novel therapeutic strategies able to exploit the natural regenerative potential of bone and that can be delivered in a less invasive manner. Among the materials studied for the development of novel scaffolds, stimuli-responsive gels containing hydroxyapatite and carbon nanotubes as nanofillers have generated great interest. In the present work, chitosan gels containing chitosan grafted CNTs and chitosan–hydroxyapatite complex have been formed by cross-linking with glycerol phosphate. The addition of the nanofillers afforded hydrogels with a faster sol/gel transition at 37 °C and enhanced mechanical properties. The thermosensitive composite gels also showed a good bioactivity profile associated with potential for the prolonged delivery of protein drugs. The inclusion of chemically cross-linked CNTs and HA in thermosensitive gels afforded injectable composite materials with enhanced properties, including reduction of gelation time, improved mechanical properties, good bioactivity, and prolonged drug release.