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.