Objectives: This study examined the timing of menarche and spermarche and their associations with physical activity (PA) and sedentary behavior (SB) after controlling for body mass index (BMI). Methods: Multiple logistic regression analyses were conducted to determine whether the timing of menarche in girls and spermarche in boys is associated with PA and SB independent of BMI in a nationally representative sample of Korean adolescents (13–18 years; N = 74,186). Results: After controlling for age, family economic status, and BMI, early timing of spermarche among boys was associated with a higher likelihood of engaging in PA and a lower likelihood of engaging in SB for < 2 hours during weekdays. By contrast, boys with late timing of spermarche were less likely to engage in PA and more likely to engage in SB for < 2 hours. Among girls, early or late timing of menarche was associated with a higher likelihood of engaging in PA and a lower likelihood of engaging in SB. Conclusion Timing of menarche in girls and spermarche in boys could be a marker for PA and SB among Korean adolescents. To promote PA and discourage SB among Korean adolescents, school-based, grade-specific interventions can be tailored by the absence or presence of menarche/spermarche.