Background: Containment measures for COVID-19 have affected surgical training globally. We sought to assess how neurosurgical training has been affected across Africa in April 2020. Methods: A cross-sectional survey was distributed to African Neurosurgical trainees seeking to review demographics and effects of COVID on training. Results: A total of 123 neurosurgery trainees responded from 23 African countries and a further 6 were abroad. A total of 91.80% were men, and 96.70% were training in public institutions. Only 41% had received training in COVID-19 with 61.79% worried that they would contract COVID-19 while performing their clinical duties. There was a marked reduction in clinical activities including a median reduction of elective surgery (−80%), clinics (−83%), and emergency surgery (−38.50%). A total of 23.58% of residents did not receive a formal salary, with 50% on less than $1000 USD gross per month. Conclusions: This is the first continental survey of neurosurgery trainees in Africa. COVID-19 has significantly affected clinical and learning opportunities. There are concerns of the long-term effects on their training activities for an uncertain period of time during this pandemic. Although there has been a global increase in e-learning, there is need to evaluate if this is accessible to all trainees.