Background: Heterogeneity of estrogen receptor (ER) expression has long been challenges for diagnosis and treatment strategy of metastatic breast cancer (MBC). A novel convenient way of ER detection using ¹⁸F-fluoroestradiol positron emission tomography/computed tomography (¹⁸F-FES PET/CT) offers a chance to screen and analyze MBC patients with ER uncertainty. Methods: MBC patients who received ¹⁸F-FES PET/CT were screened and patients with both FES positive (FES+) and negative (FES-) lesions were enrolled in this study. Progression‐free survival (PFS) was estimated by Kaplan-Meier method and compared by log-rank test. Results: A total of 635 patients were screened and 75 of 635 (11.8%) patients showed ER uncertainty. 51 patients received further treatment and were enrolled in this study. Among them, 20 (39.2%) patients received chemotherapy (CT), 21 (41.2%) patients received endocrine-based therapy (ET) and 10 (19.6%) patients received combined therapy (CT+ET). CT showed better progression-free survival (PFS) compared to ET (mPFS 7.1 vs 4.6 months, HR 0.44, 95% CI 0.20-0.93, P = 0.03). CT+ET did not improve PFS compared to either CT or ET alone (mPFS 4.4 months, P > 0.2). Conclusions:¹⁸F-FES PET/CT could identify patients with ER heterogeneity. Patients with ER uncertainty showed better sensitivity to CT rather than ET. Combined therapy of CT+ET did not improve treatment outcome.