Background: The proposal by the South African Health Ministry to implement HIV testing and counselling (HTC) at schools in 2011 generated debates about the appropriateness of such testing. However, the debate has been between the Ministries of Education and Health, with little considerations of the students. The main aim of the study was to assess the students’ opinions and uptake of HIV testing and counselling in general, and the acceptability of the provision of HIV testing and counselling in schools. The study also determined the association between socio-demographic characteristics, sexual behaviour, and HIV testing behaviour of the students. Methods: A survey was conducted among grade 10–12 high school students in North West and Gauteng provinces, South Africa. Seventeen high schools (nine rural and eight urban) were randomly selected for the administration of a researcher-assisted, self-administered, semi-structured questionnaire. Results: A total of 2970 students aged 14–27 years participated in the study; 1632 (55%) were girls, 1810 (61%) ever had sex, and 1271 (49.8%) had more than one sex partner. The mean age of first sexual activity was 15.6. Half (n = 1494, 50.1%) had been tested for HIV. Having multiple sexual partners, age, and gender were significantly associated with increased odds of having had a HIV test. Fear, being un-informed about HTC, and low HIV risk perceptions were the reasons for not getting tested. The acceptability of HTC at school was high (n = 2282, 76.9%) and 2129 (71.8%) were willing to be tested at school. Appropriateness, privacy, and secrecy were the main arguments for and against HTC at school. One-third (n = 860, 29%) had intentions to disclose their HIV status to students versus 1258 (42.5%) for teachers. Stigma, discrimination and secrecy were the primary reasons students did not intend to disclose. Conclusions: A high acceptability of HTC and willingness to be tested at school suggest that HIV prevention programs tailored to youth have a high potential of success given the readiness of students to uptake HTC. Bringing HIV testing to the school setting will increase the uptake of HTC among youth and contribute towards efforts to scale up HTC in South Africa.