Objectives We examined the potential influence of both sample selection effects and Hawthorne effects in the behavioural HIV Prevention Trial Network 068 study, designed to examine whether cash transfers conditional on school attendance reduce HIV acquisition in young South African women. We explored whether school enrolment among study participants differed from the underlying population, and whether differences existed at baseline (sample selection effect) or arose during study participation (Hawthorne effect). Methods We constructed a cohort of 3889 young women aged 11-20 years using data from the Agincourt Health and socio-Demographic Surveillance System. We compared school enrolment in 2011 (trial start) and 2015 (trial end) between those who did (n=1720) and did not (n=2169) enrol in the trial. To isolate the Hawthorne effect, we restricted the cohort to those enrolled in school in 2011. Results In 2011, trial participants were already more likely to be enrolled in school (99%) compared with non-participants (93%). However, this association was attenuated with covariate adjustment (adjusted risk difference (aRD) (95% CI): 2.9 (− 0.7 to 6.5)). Restricting to those enrolled in school in 2011, trial participants were also more likely to be enrolled in school in 2015 (aRD (95% CI): 4.9 (1.5 to 8.3)). The strength of associations increased with age. Conclusions Trial participants across both study arms were more likely to be enrolled in school than non-participants. Our findings suggest that both sample selection and Hawthorne effects may have diminished the differences in school enrolment between study arms, a plausible explanation for the null trial findings. The Hawthorne-specific findings generate hypotheses for how to structure school retention interventions to prevent HIV.