Intravenous ferric carboxymaltose (IV-FCM) can effectively correct perioperative anemia in patients undergoing major surgeries. However, its efficacy and side effects in patients undergoing free flap-based breast reconstruction are yet to be investigated. At our institution, from year 2020, patients with breast cancer undergoing abdominal free flap-based breast reconstruction were injected 500 mg of IV-FCM immediately post-operation. Propensity-matched 82 IV-FCM injected (study group) and 164 historical control group patients were retrospectively analyzed for transfusion rates, changes in hematological parameters, and flap or donor-site related complications. The major and minor complication rates related to the operation site were similar between the two groups. There was no significant difference in the transfusion rate between the two groups (control 29.9% vs. study 32.9%, p = 0.71). However, the total amount of transfusion required was significantly higher in the historical control group (control—53.2% 1 pack, 42.6% 2 packs, 4.3% 3 packs of RBC vs. Study—66.7% 1 pack, 33.3% 2 packs, p = 0.02) than in the study group. Additionally, the historical control group showed a significantly higher drop in red blood cell count, hemoglobin, and hematocrit levels from postoperative days 1–2 and 2–3 compared to the study group. Immediate postoperative use of IV-FCM in free flap-based breast reconstruction was well tolerated by patients and reduced overall transfusion volume.