Background During puberty, a gender shift in asthma prevalence occurs, with a preponderance of boys before puberty. The mechanisms underlying this gender shift are unclear. Objectives We assessed associations of pubertal stages and transition through puberty with (1) the prevalence, incidence, and remission of asthma in male and female subjects; (2) total IgE levels; and (3) peak expiratory flow (PEF) fall during a shuttle run test (SRT). Methods In the TRacking Adolescents' Individual Lives Survey study (n = 2,230; 51% female subjects), associations between pubertal stages and the prevalence, incidence, and remission of asthma were tested by using logistic regression and generalized estimating equations at a mean age of 11.1 (SD, 0.6), 13.6 (SD, 0.5), and 16.3 (SD, 0.7) years. Multiple linear regression analyses were used to study log-transformed total IgE levels and PEF fall during a SRT dependent on early versus late pubertal stages at a mean age of 16.3 years. Results The prevalence of asthma was similar in boys (7.7%) and girls (7.4%) at a mean age of 11.1 years. The prevalence of asthma was significantly higher in female (6.2%) than male (4.3%) subjects at 16.3 years of age. There were no significant associations between transition of pubertal stages and the presence of asthma, either cross-sectionally or longitudinally. Pubertal stages and log-transformed total IgE levels or PEF fall during a SRT at age 16.3 years were not correlated. Conclusions A shift in the prevalence of asthma occurs between 11.1 and 16.3 years, which is due to both an increased incidence and decreased remission of asthma in female compared with male subjects. Pubertal stages could not be proved to explain the gender shift in asthma prevalence.