In this work, chitosan hydrogels crosslinked with genipin and reinforced with cellulose nanocrystals (CNC) were developed and characterized with the aim of future biomedical applications. CNC was produced by acid hydrolysis and characterized by atomic force microscopy (AFM). Chitosan/CNC nanocomposite hydrogels were produced with different CNC concentrations (w/w): 0%, 2%, 4%, and 6%. The genipin was used as a crosslinking agent in a genipin/chitosan molar proportion of 1:8. The hydrogels were characterized by porosity measurements, scanning electron microscopy (SEM), swelling test, and mechanical compression test. No significant differences were observed concerning the porosity of the hydrogels; however, a trend of decreasing porosity was observed with increasing CNC content. The SEM images showed a better pore structure as the CNC concentration increased. A decrease in the swelling degree with increasing CNC content in the chitosan/CNC nanocomposite hydrogel was verified in the swelling tests. An increase in the CNC concentration in the chitosan/CNC nanocomposite hydrogel caused a gradual increase in the maximum stress and maximum strain as observed in the compression tests, showing a significant difference between chitosan/CNC 6 wt % and neat chitosan hydrogel.