Despite progressive policies and frameworks on school safety by the Department of Basic Education, safety remains a concern in South African schools. A cross-sectional descriptive design was employed using the National School Safety Framework (NSSF) 152-question learner survey, exploring perceptions and experiences pertaining to eight safety domains: dangerous objects, drugs and alcohol, bullying, verbal abuse, physical violence, discrimination, sexual violence, and journey to and from school. Grade 9-11 learners from 15 government-funded high schools in the Girls Achieve Power trial in Khayelitsha, Soweto, and Thembisa townships were surveyed (March 2018 - April 2019), sampling 10% of the school population. Data analysis included Principal Component Analysis (PCA), reducing correlated variables into fewer questions, then analysis on a scree plot by calculating eigenvalues; repeated PCA with those that had a minimum eigenvalue of 1 and Cronbach Alpha test for internal reliability. Eleven composite variables were included in the final analysis. In total, 1034 learners completed the NSSF learner survey; 52.9% were female and the mean age was 16 years (SD=1.36). Results show statistically significant associations between four of the 11 composite variables in relation to sex. Over half (55%) of males have experienced peer provocation and relational aggression (p<0.001). Fifty-eight percent of females reported feeling unsafe on their way to and from school (p<0.003). Over half of males reported that their school was not effective in enforcing discipline (p=0.002) while 58% of females noted they could comfortably report any form of experienced or witnessed violence at school, to their educators (p<0.000). Violence continues to be a concern in South African schools. Interventions should work across the ecological model to effectively prevent and reduce violence at school and community levels. Strengthened NSSF implementation is critical to achieving this. We recommend NSSF learner survey adaptations to increase utility and implementation.