Molecular dynamics (MD) simulations were performed to calculate the interaction between chitosan at different degrees of deacetylation (DD) and carbon nanotubes (CNTs) functionalized with either amine (−NH2) or carboxylic (−COOH) groups. The objective was to elucidate the effect of the CNT functionalization type and the different DD of chitosan on the mechanical properties of the nanocomposite. For a certain DD, where the glucosamine and acetyl-glucosamine units are uniformly distributed along the chitosan chain, MD simulations showed that this molecule depicts a large contacting superficial area that allows the interaction with the functionalized CNT. It was also found that the attractive interaction between a 50% DD chitosan and the −NH2 functionalized CNT (CNT–NH2) was the strongest among the different deacetylated cases under study. For the 50% DD case, a wrapping effect of the CS chain around the CNT–NH2 structure was displayed which was attributed to hydrogen bonds formation between the amine groups in the CNT and the −OH and −NH2 groups in the chitosan molecule. Composite films of chitosan, reinforced with multiwall carbon nanotubes (MWCNT) functionalized with either −NH2 (MWCNT–NH2) or −COOH (MWCNT–COOH), were prepared to measure their Young’s module. The experiments showed that the films reinforced with MWCNT–NH2 exhibited larger Young’s modules than those functionalized with −COOH groups. The above was due, likely, to the strong interaction between the amino functionalized CNTs and the polymeric matrix. The simulation results were in agreement with the experimental data.