Prolonged mobile phone use (MPU) is prevalent in adolescents. This study examined the associations between prolonged MPU and academic performance in Chinese adolescents. Participants were 11,831 adolescents who participated in the Shandong Adolescent Behavior and Health Cohort in 2015. We used a self-administered questionnaire to collect data on demographics, weekday and weekend MPU, sleep duration, insomnia, depression, and academic performance. We obtained a subsample’s year-end achievement test scores for Chinese, Mathematics, and English, 3 months after baseline survey ( = 856). Results showed that with prolonged MPU from ≥1 hour/day on weekdays and ≥2 hours/day on weekends, the prevalence of self-reported poor academic performance significantly increased, and the achievement test scores significantly decreased. After controlling for adolescent and family covariates, students who used mobile phone ≥2 hours/day on weekdays (OR = 2.12, 95% CI = 1.82-2.47) and ≥5 hours/day on weekends (OR = 1.50, 95% CI = 1.31-1.72) were significantly more likely to report poor overall academic performance and scored significantly lower on Mathematics and English compared with those who used mobile phone <1 hour/day on weekdays and <2 hours/day on weekends, respectively. The mediating effects of reduced sleep duration, insomnia, and depression on the association between prolonged MPU and academic performance was small. In conclusion, prolonged MPU is associated with poor academic performance as measured by self-reports and subject tests in Chinese adolescents. Our findings suggest that adolescents should be advised to limit the time of MPU to minimize its harmful effects on sleep, mental health, and academic performance.