Patients with fibromyalgia (FM) show widespread pain associated with other symptoms such as cognitive problems, depression, and anxiety among others associated with alterations in the central nervous system. The hippocampal subfields had differences in function, histology, and connectivity with other brain regions, and are altered in different diseases. This study evaluates the volumetric differences between patients with FM compared with a healthy control group. A total of 49 women with, and 43 healthy women completed this study. T1-weighted MRI was used to assess brain volume, and FreeSurfer software was used to segment the hippocampal subfields. Women with FM had a significant reduction in most of the hippocampal subfields. The regression equation models were obtained to predict the volume of specific subfields of the right and left hippocampus. These findings provide that women with FM have lower hippocampal subfields volumes compared with healthy women. Besides, regression models show that different covariates, such as age, cognitive impairment, or depression, are related to specific subfields.