Background Reconstruction after removal of a malignant tumor in the head and neck region is crucial for restoring tissue integrity, function, and aesthetics. We retrospectively analyzed patients who underwent intraoral reconstruction surgery using radial forearm free flaps (RFFF) and anterolateral thigh free flaps (ALT) at a single institution to provide more information supporting the choice of a reconstruction method after removal of head and neck cancer. Methods The charts of 708 patients who underwent head and neck reconstruction between 1998 and 2018 at the Department of Plastic and Reconstructive Surgery at our institution were retrospectively reviewed. Patients’ age, sex, and history of radiation therapy, diabetes mellitus, and smoking were retrieved. The primary cancer site, types of defects, and complications were investigated. Results Overall, 473 and 95 patients underwent reconstruction surgery with RFFF and ALT, respectively. RFFF was more often used in patients with cancers of the pharynx, larynx, esophagus, or tonsil, while ALT was more frequently used in patients with cancers of the mouth floor with tonsil or tongue involvement. The proportion of patients undergoing ALT increased gradually. Flap failure and donor site morbidities did not show significant differences between the two groups. Conclusions RFFF and ALT flaps resulted in similar outcomes in terms of flap survival and donor site morbidity. ALT can be an option for head and neck reconstruction surgery in patients with large and complex defects or for young patients who want to hide their donor site scars.