Objective: The purpose of this study was to investigate the role of [68Ga]Ga-DOTA-FAPI-04 PET/CT in evaluating ovarian physiological FDG uptake. We also prospect future research. Design: Retrospective study. Setting: Nuclear Medicine Department of the Affiliated Hospital of Southwest Medical University. Sample: female patients who underwent simultaneous [18F]-FDG PET/CT and [68Ga]Ga-DOTA-FAPI-04 PET/CT examinations in the Affiliated Hospital of Southwest Medical University from September of 2020 to January of 2021. Methods: We reviewed the data of 78 female patients who underwent [18F]-FDG and [68Ga]Ga-DOTA-FAPI-04 PET/CT scanning within 3 days and selected those whose ovaries showed abnormal FDG activity. Patients with ovarian lesions confirmed by pathological biopsy or clinical follow-up were excluded, and the uptake of imaging agents was semi-quantitatively analyzed. Main outcome measures: Characteristics of ovarian imaging agent uptake on 18F-FDG and 68Ga-DOTA-FAPI-04 PET/CT images, pathological data, and clinical follow-up evidence. Results: This study included 14 patients who were diagnosed with physiological ovarian FDG uptake by pathology or at least 6 months follow-up. The average age was 38.6 years old (range, 19-52). Physiological ovarian uptake of FDG was more common in unilateral cases, with a median SUVmax of 4.8±1.8 (range, 2.7-8.2). There was no ovarian uptake of the imaging agent on FAPI imaging. Conclusion: Our study showed that FDG, but not FAPI, uptake increased in normal ovaries due to the influence of the menstrual cycle. [68Ga]Ga-DOTA-FAPI-04 PET/CT has a unique advantage in differentiating the ovarian physiological [18F]-FDG uptake and can better identify ovarian lesions.