Several animal or case reports have demonstrated that methylphenidate (MPH) disrupts endogenous gonadal hormones and interferes with the pubescent development of children with attention-deficit/hyperactivity disorder (ADHD). Therefore, this prospective study examined the changes in gonadal hormones and pubescent development in children with ADHD undergoing 12-month MPH treatment. We recruited 146 patients with ADHD (mean age: 8.9 years, 76.7% males) and 70 healthy controls (mean age: 9.2 years, 65.7% males). Blood samples were obtained to measure the serum levels of sex hormone-binding globulin (SHBG), follicle stimulating hormone (FSH), luteinizing hormone (LH), estradiol, progesterone, testosterone, free testosterone, and prolactin in each child. The sex maturation of ADHD patients was evaluated using the Tanner Stage. Patients with ADHD (107 received MPH treatment and 39 were under natural observation) were followed up for 12 months, and we re-examined hormone levels and Tanner Stage at the endpoint. During a 12-month follow-up for all ADHD patients, the serum levels of SHBG and progesterone significantly decreased, while LH, FSH, and free-testosterone levels significantly increased. However, the duration, drug formulations, and doses of the MPH treatment did not significantly influence gonadal hormone trends or changes of Tanner Stage. This study provides evidence about gonadal hormone trends and pubescent development in children with ADHD who receive long-term MPH treatment in natural settings. We suggest that MPH treatment at usual doses does not significantly alter gonadal function trends in ADHD patients over the course of one year.