Human physiological signals have been widely used to non-invasively measure cognitive load (CL) during task execution. A major challenge for CL detection is the presence of stress, which may affect physiological measurements in ways that confound reliable detection of CL. In this experiment we investigated the effect of stress on cognitive load measurement using galvanic skin response (GSR) as a physiological index of CL. The experiment utilized feelings of lack of control, task failure and social-evaluation to induce stress. Mean GSR values were shown to be significantly different between CL levels in the ‘no-stress’ condition, but not when including the ‘stress’ condition. On the other hand, features extracted from GSR signals based on peak detection exhibited consistent behaviour under both conditions, demonstrating the usefulness of the features as cognitive load index even when a person’s stress level is fluctuating.