Due to the increasing prevalence of childhood obesity, the association between classroom furniture and energy expenditure as well as physical activity was examined using a standing-desk intervention in three central-Texas elementary schools. Of the 480 students in the 24 classrooms randomly assigned to either a seated or stand-biased desk equipped classroom, 374 agreed to participate in a week-long data collection during the fall and spring semesters. Each participant’s data was collected using Sensewear^® armbands and was comprised of measures of energy expenditure (EE) and step count. A hierarchical linear mixed effects model showed that children in seated desk classrooms had significantly lower (EE) and fewer steps during the standardized lecture time than children in stand-biased classrooms after adjusting for grade, race, and gender. The use of a standing desk showed a significant higher mean energy expenditure by 0.16 kcal/min (p < 0.0001) in the fall semester, and a higher EE by 0.08 kcal/min (p = 0.0092) in the spring semester.