In this study, the optimization of different process variables—pH (4–6), aeration rate (200–550 rpm) and agitation rate (0.6–1.8 vvm) were investigated using rotating simplex method and uniform design method to enhance xylitol production from xylose by D. nepalensis in a batch stirred tank bioreactor. Maximum xylitol productivity (0.576 g L−1 h−1) was obtained at pH 4.0, agitation 300 rpm and aeration 1.5 vvm by rotating simplex method. Individual optimum values of pH, agitation and aeration are 4.2, 370 rpm and 1.2 vvm, respectively, for productivity, 4.3, 350 rpm and 1.0 vvm, respectively for xylitol concentration and 4.4, 360 rpm and 0.8 vvm, respectively for yield. Using generalized distance approach, the simultaneous optimal values were found to be—pH 4.3, 370 rpm and 0.9 vvm. After multi-response analysis, batch fermentation at optimal operating conditions resulted in enhanced productivity (0.76 g L−1 h−1), xylitol concentration (59.4 g L−1) and yield (0.58 g g−1) with an increase of 76.74 % of xylitol productivity. © 2016, The Author(s).