This study aimed to characterize energy expenditure patterns using the tri-axial accelerometer and to identify the association of energy expenditure with clinical parameters in patients with systemic lupus erythematosus (SLE). Estimates of energy expenditures represented by total activity calorie (TA), physical activity calorie (PA), total activity calorie per body weight (TABW), and physical activity calorie per body weight (PABW) of 49 female SLE patients were assessed using the RT3 tri-axial accelerometer (StayHealthy, Monrovia, CA) in a seven-day period. SLE patients in the highest body mass index (BMI) tertile showed significantly lower values of TABW compared to those in the lowest tertile, while SLE patients in the lowest TABW tertile showed significantly higher body weight, waist circumference, BMI, SLE disease activity index (SLEDAI), dosage of prednisone, and blood pressure. There was a high prevalence of metabolic syndrome and SLE patients with metabolic syndrome showed significantly lower TABW. In addition, both TABW and PABW significantly but negatively correlated with SLEDAI. In conclusion, the RT3 accelerometer is suitable for evaluating total and physical activity-related energy expenditure in patients with SLE. TABW measured by the tri-axial accelerometer is inversely related with body weight status and disease activity in SLE patients. This suggests that estimates of energy expenditure by the tri-axial accelerometer may be applied in the management of SLE.