In the current study, we evaluated the test‐retest reliability of amygdala response using an emotional face‐matching task that has been widely used to examine pathophysiology and treatment mechanisms in psychiatric populations. Activation within the fusiform face area (FFA) was also examined. Twenty‐seven healthy volunteers completed a variation of the face‐matching paradigm developed by Hariri et al. (2000) at two time points approximately 90 days apart. Estimates of test‐retest reliability of amygdala response to fearful faces were moderate, whereas angry and happy faces showed poor reliability. Test‐retest reliability of the FFA was moderate to strong, regardless of facial affect. Collectively, these findings indicate that the reliability of the BOLD MR signal in the amygdala varies substantially by facial affect. Efforts to improve measurement precision, enlarge sample sizes, or increase the number of assessment occasions seem warranted.