To study the effect of agitation speed (rpm) and dissolved oxygen concentration (DO) on the production of gamma linolenic acid by Mucor sp. RRL001, a central composite design experiment was performed in a 5-L stirred tank bioreactor. The design consisted of a total of 10 runs consisting of runs at five levels for each factor and was divided in two blocks. The ANOVA analysis and Pareto chart of effects suggested agitation speed (p = 0.0142) linear effect and DO concentration (p = 0.0342) quadratic effects were significant factors with significant contribution to the response. The validation run based on the optimum production zone in response surface plot resulted in the maximum 350.3 mg l−1 GLA yield as compared with model predicted value of 340.7 mg l−1. The study suggests that agitation rate is having more pronounced effect on GLA yield than dissolved oxygen concentration by ensuring enhanced mass transfer and by preventing wall growth at elevated agitation speed. Also, it shows that higher GLA yields can be obtained in a simple medium at moderate oxygen saturation and that the Mucor sp. RRL001 is resistant to high agitation linked shear stress and suitable for GLA production at higher scale.