Motor coordination (MC) is an essential skill underpinning precise and controlled movements, contributing significantly to daily functioning and overall performance. The developmental trajectory of MC in children is intricately shaped by a spectrum of factors encompassing age, gender, and physical activity engagement. Delving into the complex interrelation of these variables holds the potential to unravel nuanced developmental trends and offer targeted avenues for interventions aimed at augmenting motor proficiency in the pediatric population. This study aimed to assess the differences in MC of primary school students based on sex, age, and physical activity participation (PAP). A total of 848 students from public primary schools, aged between 6-9 years, including 412 boys and 436 girls. The MC was measured using Körperkoordinationstest für Kinder (KTK3+) test battery, which included Jumping sideways (JS), Balancing backward (BB), Moving sideways (MS), and Eye-Hand Coordination (EHC). One-way multivariate analysis of variance (MANOVA) was used to determine the binary and triple interactions of sex, age, and PAP variables on the MC parameters of the participants. The study revealed that boys aged 6-9 had higher scores than girls on eye-hand coordination (EHC) ( < 0.02). No significant gender-related differences in balancing backward (BB), jumping sideways (JS), and moving sideways (MS) were found. When the subtests of KTK3+ were compared by age, a significant difference was observed between the groups in all subtests ( < 0.05). With respect to PAP, students with PAP had a significant advantage in all subtests of the KTK3+ ( < 0.05). The double co-effects or triple co-effects of age, sex, and PAP parameters do not influence the KTK parameters. This study presents evidence supporting sex differences in the motor skills of children within this age range and highlights the potential impact of age and physical activity on motor development.