In this work, we demonstrate that the thiol-yne click reaction could be efficiently mediated by ultrasonic irradiation and implement the ultrasound-assisted thiol-yne click reaction to chitosan chemistry as a polymer-analogous transformation. We optimize power and frequency of ultrasound to preserve selectivity of the click reaction and avoid ultrasonic degradation of the chitosan polymer chain. Thus, we obtain a new water-soluble betaine. Using ionic gelation of the obtained betaine derivatives of chitosan, we prepare nanoparticles with a unimodal size distribution. Furthermore, we present results of antibacterial and transfection activity tests for the chitosan derivatives and their based nanoparticles. The derivative with a medium molecular weight and a high degree of substitution demonstrated the best antibacterial effect. It derived nanoparticles with a size of ca. 100 nm and ζ-potential of ca. +69 mV revealed even higher antibacterial activity, slightly superior to commercial antibiotics ampicillin and gentamicin. On the contrary, the obtained polymers possess a much more pronounced transfection activity as compared with their based nanoparticles and species with a low degree of substitution acts as the most efficient transfecting agent. Moreover, the obtained betaine chitosan derivatives as well as their derived nanoparticles are non-toxic.