Microwave-assisted extraction (MAE) of chitosan from dried fungal biomass of Rhizopus oryzae NRRL1526, obtained by culturing on potato dextrose broth (PDB), was performed and the optimal conditions required were identified using statistical analysis for the first time in this study. This microwave-assisted extraction (MAE) was compared against the conventional autoclave assisted method of chitosan extraction. The full factorial experimental design was used to investigate the impact of operating parameters of MAE, microwave power (100 W-500 W), and duration (10 min-30 min), on alkaline insoluble material (AIM) yield, chitosan yield, and degree of deacetylation (DDA). The effect of operating conditions was then evaluated using full factorial data analysis and optimum condition for MAE of chitosan was identified using response surface methodology to be 300 W and 22 min. This optimum condition identified was then further evaluated and the chitosan obtained characterized. Higher chitosan yield of 13.43 ± 0.3% (w/w) of fungal biomass was obtained when compared to that obtained, 6.67% ± 0.3% (w/w) of dry biomass, for the conventional extraction process. MAE yielded chitosan of higher degree of deacetylation, 94.6 ± 0.9% against 90.6 ± 0.5% (conventional heating), but the molecular weight was observed to be similar to that obtained by using conventional autoclave heating. MAE of chitosan was observed to yield a higher quantity of chitosan when compared to conventional extraction process and obtained chitosan exhibited a higher degree of deacetylation as well as molecular weight. The lower energy consumption of 0.11 kW h for MAE (5 kW h for conventional process) and the concomitant reduction in the energy bill to 1.1 cents from 50 cents, in addition to the above results, show that microwave irradiation is a more efficient and environment-friendly means to obtain chitosan from fungal biomass.