Postoperative delirium (POD) is a major risk factor for an extended hospital stay and higher costs, and is associated with increased mortality. The incidence of POD is high in free flap procedures, and POD may also be a risk factor for flap loss and complications. Sarcopenia is a condition characterized by skeletal muscle mass (SMM) depletion and a decrease in muscle power or physical activity. The aim of this study was to investigate risk factors for postoperative delirium (POD), including SMM, in 122 patients undergoing free flap repair after oral cancer resection. All patients underwent preoperative abdominal-lumbar CT or PET-CT. Cross-sectional areas (cm) of skeletal muscles at the third lumbar vertebra were measured on preoperative CT, normalized for height, and defined as the skeletal muscle index (SMI, cm/m). Risk factors for POD were investigated, including the value of SMI and taking the type of POD into consideration. POD occurred in 45 patients (36.9%), and was hyperactive in 28 (62.2%), mixed in 13 (28.9%), and hypoactive in 4 (8.9%). In multivariate analysis, high preoperative albumin ( = 0.046, adjusted odds ratio [OR] = 3.69) and postoperative insomnia ( < 0.001, OR = 6.79) were significant risk factors for POD. In a sub-analysis evaluating risk factors restricted to POD including the hypoactive type, lower SMI ( = 0.035, OR = 2.52 per 10-unit decrease) and postoperative insomnia ( = 0.003, OR = 6.37) were significant. We conclude that lower SMM increases the hypoactive and mixed types of POD. Increasing SMM by exercise and nutritional therapy preoperatively may prevent such POD in free flap repair for oral cancer.