Background: Patients who undergo gastrectomy for gastric cancer are susceptible to osteoporosis. To prevent a decrease in bone mineral density, an appropriate prophylaxis is considered important to adjust the post-gastrectomy condition. In this study, we will compare two different routes of administration of ibandronic acid (oral or intravenous) plus eldecalcitol as a potentially more suitable treatment for patients at a high risk of fragile fracture. Protocol: This study protocol describes a randomized, active-controlled, non-blind, single-center, phase II trial. For patients in the investigational arm (Group A), sodium ibandronate hydrate will be administered intravenously once a month with daily oral intake of eldecalcitol; for those in the control arm (Group B), sodium ibandronate hydrate will be administered orally once a month with daily oral intake of eldecalcitol. We will recruit patients aged 45–85 years who have undergone gastrectomy for gastric cancer and are at a risk of fragility fractures. The study will include patients with existing vertebral fractures and/or femoral proximal fractures, or with lumbar and/or proximal femur bone mineral density of less than 80% of the young adult mean. The primary outcome of this study will be the change in lumbar bone mineral density. We will also evaluate the changes in femur bone mineral density, bone metabolism markers, health-related quality of life as evaluated using the EuroQol 5 Dimension (EQ-5D), and digestive symptoms as evaluated using the Gastrointestinal Symptom Rating Scale after 52 weeks of treatment. Conclusions: We believe that appropriate treatments that are adjusted to the condition of patients after gastrectomy are important for the prevention of bone mineral loss. Registration: This study was accepted by the Japan Registry of Clinical Trials (jRCT1041200059, November 6, 2021).