The purpose of this systematic review was to examine the effects of active desks in the school setting on sedentary behavior, physical activity, academic achievements and overall health among children and adolescents aged 5–17 years. A systematic literature search was conducted using five databases until October 2020. Twenty-three studies were included. Studies reported an increase of around 36% in energy expenditure for cycling desks and between 15% and 27.7% for upright active desks. Children increased inhibitory control and selective attention capacity while using cycling desks. A heterogeneous quality of design and of results were observed limiting comparisons and conclusions for each active desk. Despite the lack of strong methodology for the included studies, active desks appear to be a promising intervention in classrooms to improve health-related outcomes in children aged 5–17 years. Due to weak methodology, future studies with stronger study designs and methodology are needed to better inform policy and practice about the role of classroom active desks on health-related outcomes in children and adolescents.