Purpose <p>Since the avid uptake of ⁶⁸Ga-labeled fibroblast activation protein inhibitor (⁶⁸Ga-FAPI-04) observed in female reproductive organs, our objectives were to investigate the physiological uptake characteristics and provide preliminary reference ranges for clinical use.</p> Procedures <p>We reviewed the findings of female patients who underwent ⁶⁸Ga-FAPI-04 PET/CT at our institution between April 2022 and June 2023. The standard uptake value (SUV) of reproductive organs and menstrual information were collected. All patients were categorized into reproductive period group, perimenopause group, and postmenopause group. We analysed the uptake levels among the three groups, and their association with age and menstrual cycle.</p> Results <p>A total of 109 patients were included in this study. Higher ovarian SUVs were detected in reproductive patients (SUV_right: 2.75 ± 0.84, IQR: 1.39—5.26; SUV_left: 2.72, IQR: 2.34—3.20; <i>p</i> = 0.315) than in postmenopausal patients (SUV_right: 2.27, IQR: 2.01—2.75; SUV_left: 2.38 ± 0.55, IQR: 1.35—3.60; <i>p</i> = 0.767), as well as uterine ⁶⁸Ga-FAPI-04 accumulations. The SUVs of uterine fundus and corpus were approximately three times higher than that of the cervix. In reproductive period group, higher SUVs were observed in bilateral ovaries around the ovulatory phase to the early luteal phase, and higher uterine SUVs were noted in the menstrual and proliferative phases. The SUVs in all reproductive organs (except the ovaries) showed significant negative correlations with age in all patients (all <i>p</i> &lt; 0.01).</p> Conclusions <p>⁶⁸Ga-FAPI-04 SUVs in reproductive organs are higher in premenopausal patients than in postmenopausal patients. The ⁶⁸Ga-FAPI-04 accumulation in reproductive organs might be associated with menstrual cycle. Including more patients from different menstrual phases could contribute to investigating the uptake characteristics and their underlying mechanisms.</p>