Nearly all functional magnetic resonance imaging (fMRI) studies are conducted in the supine body posture, which has been discussed as a potential confounder of such examinations. The literature suggests that cognitive functions, such as problem solving or perception, differ between supine and upright postures. However, the effect of posture on many cognitive functions is still unknown. Therefore, the aim of the present study was to investigate the effects of body posture (supine vs. sitting) on one of the most frequently used paradigms in the cognitive sciences: the N-back working memory paradigm. Twenty-two subjects were investigated in a randomized within-subject design. Subjects performed the N-back task on two consecutive days in either the supine or the upright posture. Subjective sleep quality and chronic stress were recorded as covariates. Furthermore, changes in mood dimensions and heart rate variability (HRV) were assessed during the experiment. Results indicate that the quality of sleep strongly affects reaction times when subjects performed a working memory task in a supine posture. These effects, however, could not be observed in the sitting position. The findings can be explained by HRV parameters that indicated differences in autonomic regulation in the upright vs. the supine posture. The finding is of particular relevance for fMRI group comparisons when group differences in sleep quality cannot be ruled out.