Although educational kinesiology is a popular intervention aims to improve brain functioning via physical movements, it lacks supporting scientific evidence. This study explores the effect of educational kinesiology on the changes in stress and anxiety markers in kindergarteners with special needs using psychometrics and biological measures. This open label non-randomized clinical trial was registered retrospectively in the Chinese Clinical Trial Registry (registration number: ChiCTR2000036305, url: http://www.chictr.org.cn/showproj.aspx?proj=58067, registration date: 22/08/2020). Thirty-seven kindergarteners with special needs (3.5-6.5 years old) were assigned to either the intervention group, which received one-hour educational kinesiology intervention weekly for a total of 10 weeks, or the wait-list control group. Scores of Parent-rated Preschool Anxiety Scale (PAS-TC), salivary cortisol and oxytocin levels were obtained pre- and post-intervention. After controlling baseline, the changes in oxytocin levels remained significantly different between groups (F1,35 = 5.590, p = 0.020, eta2 = 0.145), but not in cortisol levels (F1,35 = 0.364, p = 0.550, eta2 = 0.01). PAS-TC showed significant improvement in anxiety levels after the intervention in the intervention group (X2 = 4.367, p = 0.037, φ = 0.344, p = 0.037). Findings from both subjective and objective measures indicate a plausible anti-stress and anxiety effect in kindergarteners with special needs.