This analysis examined trends in self-reported sexual and reproductive health behaviours among New Zealand secondary school students, using findings from nationally representative health and wellbeing surveys conducted in 2001 (n=9699), 2007 (n=9107) and 2012 (n=8500). Logistic regression analyses revealed significant reductions over time in certain sexual outcomes: ‘Ever had sex’ (−6.9%; p<0.001); ‘currently sexually active’ (− 2.3%; p<0.001); ‘always use condoms’ (−3.3%; p=0.006); ‘condoms at last sex’ (−7.0; p=0.002); ‘contraception at last sex’ (−5.8%; p<0.001) and sexually transmitted infections (−0.3%; p=0.001). However, there was no significant change over time in ‘Always use contraception’ (−1.4%, p=0.514). In 2012, Māori (OR 0.7), Pacific (OR 0.5) and socioeconomically deprived students (OR 0.7) were less likely to use condoms than students in 2001. Moreover, Māori (OR 0.6), Pacific (OR 0.4), Asian (OR 0.5), younger (OR 0.6), and socioeconomically deprived (OR 0.6) students were less likely to use contraception, compared to students in 2001.