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Abstract Background Follow-up programs for gynecological cancer patients are currently under revision. There is limited evidence that traditional follow-up and clinical examinations improve survival in an early-stage gynecological setting. Further, traditional follow-up programs fail to accommodate the patient’s need for psychosocial and sexual supportive care and to actively involve patients and their relatives in the follow-up process. Individualized programs may replace traditional routine follow-up with fixed intervals and length. Focusing on alarm-symptoms and self-reporting may ensure detection of recurrence while allowing a continuous attention to the patient’s well-being and return to daily life. In this study, a nurse-led, individualized, and need-based intervention with a specific focus on patient empowerment is tested against a standard physician-led model primarily focusing on the detection of recurrence. Methods The study is designed as a clinical, randomized trial conducted in one of four national onco-gynecological centers in Denmark. Patients with early-stage cervical or endometrial cancer are eligible for inclusion. The intervention group undergoes individualized, nurse-led follow-up supporting patient empowerment including repeated use of electronic patient-reported outcome measures (ePROMs) before each contact as a dialogue support tool. The follow-up contacts are mainly conducted by telephone. All project nurses attended a special training program before project start and are all well-educated and dedicated onco-gynecological nurses. The control group receives standard, physician-led, follow-up without use of ePROMs or specific focus on empowerment. The effect of the intervention is evaluated by questionnaires completed by patients at baseline (3 months after surgery) and 12, 18, and 36 months after surgery. Outcomes include empowerment using the Skill and technique subscale of the HEI-Q questionnaire as the primary outcome while fear of cancer recurrence and health-related quality of life as well as the remaining subscales of the HEI-Q represent secondary outcomes. Data is collected by use of the REDCap technology, which also provides a customized visual support function for the dialogue tool. Discussion This study will provide new information about follow-up in early-stage gynecological cancer settings and thereby contribute to improvement of future follow-up programs. Importantly, the study will provide knowledge about the impact of specific focus on patient empowerment in follow-up programs and, further, how to facilitate empowerment among patients. Trial registration The study is registered at clinicaltrials.gov: ID no. NCT03838861. Registered on 6 February 2019. Protocol version 2, issue date 21 November 2022.