South African children have a right to equitable education free from harm. Still, news of school bullying incidents continues to grab South African news headlines. Creating a safe environment conducive to learning is vital in learners’ mathematics achievement (MA). We investigated the association between bullying and Grade 9 MA in South African schools. We followed a quantitative design with a research paradigm of positivism and a secondary data analysis study design. We analysed TIMSS 2019 data and proposed a model containing 21 constructs; 20 independent variables (gender, socio-economic status (SES) and 18 variables about bullying) and one dependent variable (MA). The multi-level analysis showed refusing to talk to learners, insulting their families, making them do things they didn’t want to do, sending nasty, hurtful messages or embarrassing photos of them online, physically hurting them, saying mean things about their physical appearance, stealing from them, physical injury to other learners and SES are significant predictors of MA. Learners must be reminded that there are clear regulations in place to penalise bullies. Due to the exponential growth of e-Learning over the past two years as a result of COVID-19, we recommend the incorporation of cyber-safety and cyber-protection techniques into every learner-teacher training.