The aim of this study was to investigate the potential value of dual tracers 18F-FDG and 18F-FES PET/CT in predicting response to Cyclin-Dependent 4/6 Kinase (CDK4/6) inhibitors combined with endocrine therapy for metastatic estrogen receptor (ER)-positive breast cancer patients. This retrospective study enrolled 38 ER-positive metastatic breast cancer patients from our center who underwent both 18F-FDG and 18F-FES PET/CT scans within 1month before CDK4/6 inhibitors combined with endocrine therapy. The extracted parameters comprised the maximum standardized uptake value (SUVmax) for both FDG and FES PET, as well as the ratio between FES and FDG SUVmax. Each parameter was dichotomized based on its median threshold. The primary endpoint was progression-free survival (PFS), which was estimated using the Kaplan-Meier method and compared by the log-rank test. After a median follow-up of 15.6months, progressive disease was observed in 23 out of 38 patients, and the median PFS for the whole cohort was 21.0months [95% confidence interval (CI) 12.7-29.3]. FES and FDG PET identified 6 patients (15.8%) with FES-negative lesions, suggesting ER heterogeneity in metastatic lesions. The median PFS of these patients was only 5.3months (95% CI 1.7-8.9), which was substantially shorter than that of patients with 100% FES-positive lesions (median PFS 22.9months, 95% CI 17.1-28.7, P < 0.001). Patients with 100% FES-positive lesions who had high FES/FDG showed significantly shorter PFS compared to those with low FES/FDG (14.9 vs. 30.5months, P = 0.003). This study shows that FDG and FES PET imaging may serve as valuable tools for patient selection in the context of CDK4/6 inhibitor therapy combined with endocrine treatment, and have the potential to function as prognostic biomarkers.