Background: Electronic media use is increasing in low- and middle-income countries, thus we aim to investigate the prevalence of different aspects of e-media use and its association to symptoms and neurocognitive outcomes in rural South Africa. Methods: In the cohort study, “Child health Agricultural Pesticide study in South Africa (CapSA)”, of 1001 children and adolescents, aged 9–16 years, we enquired at baseline about the following aspects of e-media use: (1) call duration (2) total screen time (3) night-time awakenings from mobile phone use, and (4) Mobile Phone Problematic Use. Four health outcomes were included: sleep disturbance, health related quality of life (HRQoL), headaches and cognitive performance, assessed through six tests on domains of attention, memory and processing speed, using the iPad-based software, CAmbridge Neuropsychological Test Automated Battery (CANTAB). Linear regression analysis adjusted for relevant confounders was conducted with categorized exposure variables low, medium and high use. Results: One third of the cohort (31.8%) are mobile phone users reporting average duration of calls per day up to 75 min (mean = 2.5 mins; SD = 8.9 mins). Amongst 46% of the cohort who report e-media device use, total screen time ranged from 1 min to 441 min (mean = 28.3; SD = 53.0). Findings Amongst those reporting regular night-time awakenings (≥1 times per week) from mobile phones, HRQol declined by 2.9 (95% CI: −6.1, 0.3), the sleep disturbance score increased by 2.0 (1.1, 2.9) units and headache impact score significantly increased by 5.4 (2.6; 8.2) units compared to non-exposed. Cognitive performance scores tended to be slightly improved mostly in moderate e-media users. The reaction response speed was consistently improved amongst all four exposure groups compared to non-users. Conclusion: These results are among the first from Africa on benefits and risks associated with e-media use. Our findings imply that with regard to the education of adolescents, a vigilant balance is needed to profit from the beneficial effects of moderate e-media use on cognition, while preventing the negative side effects for HRQoL, sleep disturbance and headache severity.