Background To compare the diagnostic accuracy of 18F-fluoroestradiol (18F-FES) and 18F-fluorodoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) for breast cancer recurrence in patients with estrogen receptor (ER)-positive primary breast cancer.Methods Our database of consecutive patients enrolled in a previous prospective cohort study to assess 18F-FES PET/CT was reviewed to identify eligible patients who had ER-positive primary breast cancer with suspected first recurrence at presentation and who underwent 18F-FDG PET/CT. The diagnostic accuracy of qualitative 18F-FES and 18F-FDG PET/CT interpretations was assessed, comparing them with histological diagnoses.Results Of the 46 enrolled patients, 45 were confirmed as having recurrent breast cancer, while one was diagnosed with chronic granulomatous inflammation. Forty (89%) patients were ER-positive, four (9%) were ER-negative, and one (2%) patient did not undergo an ER assay. The sensitivity of 18F-FES PET/CT was 71.1% (32/45, 95% CI: 55.7–83.6), while that of 18F-FDG PET/CT was 80.0% (36/45, 95% CI: 65.4–90.4) when malignant interpretation was defined as positive, and 93.3% (42/45, 95% CI: 81.7–98.6) when an equivocal or malignant interpretation was considered positive. There was no significant difference in sensitivity between 18F-FES and 18F-FDG PET/CT (P=0.48) when malignant 18F-FDG interpretation was considered positive, but the sensitivity of 18F-FDG was significantly higher than 18F-FES (P=0.013) when equivocal or malignant interpretation was considered positive. One patient with a benign lesion showed negative 18F-FES but malignant 18F-FDG uptake.Conclusions The restaging of patients who had ER-positive primary breast cancer and present with recurrent disease may include 18F-FES PET/CT.