Functional magnetic resonance imaging (fMRI) is an increasingly important tool in psychological research, but its reliability is somewhat undermined by concerns about the fMRI environment’s impact on cognition. The unusual scanner environment, presenting a combination of stressors including high intensity noise, enclosed space, and restricted motion, is thought to impair participants’ cognitive performance during an fMRI session. To investigate the effect these stressors have on working memory, this study presented 20 participants with two working memory measures, the operation span (ospan) and the n-back, in both a standard laboratory setting and a full-scale fMRI simulator. Comparing subjects’ results in each condition, ospan performance was significantly lower in the simulator setting while the difference in n-back performance was insignificant. Analysis of these results suggests the fMRI environment can negatively impact upon cognitive performance, but that this effect varies across different tasks. The results also imply a fundamental distinction between the n-back and the ospan. These findings are significant for the interpretation of fMRI images and the use of working memory tasks in neuroimaging research, and indicate a need for further research into the effects of the fMRI environment on cognition.