Objective: To investigate prevalence and trends in key mental health and well-being indicators among New Zealand secondary school students. Methods: Representative cross-sectional youth health surveys with 2–4% of the New Zealand secondary school population were conducted in 2001, 2007, 2012 and 2019 (total n = 34,548). Results: In 2019, 69.1% reported good well-being (95% confidence interval = [67.6, 70.6]; World Health Organization 5-item), 22.8% reported clinically significant depression symptoms (95% confidence interval = [21.4, 24.1]; Reynolds Adolescent Depression Scale–Short Form) and 41.8% reported possible anxiety symptoms (95% confidence interval = [40.5, 43.2]; Generalized Anxiety Disorder 2, adapted). Past-year prevalence of periods of low mood (38.3%, 95% confidence interval = [36.6, 40.1]), deliberate self-harm (24.1%, 95% confidence interval = [22.8, 25.4]), suicide thoughts (20.8%, 95% confidence interval = [19.2, 22.4]) and suicide attempts (6.3%, 95% confidence interval = [5.5, 7.0]) were observed. After relative stability from 2001 to 2012, there were large declines in mental health to 2019. The proportion reporting good well-being decreased (odds ratio 0.71, 95% confidence interval = [0.65, 0.78], p < 0.001), depression symptoms increased (odds ratio 1.96, 95% confidence interval = [1.75, 2.20], p < 0.001) and past-year suicide thoughts and suicide attempts increased (odds ratio 1.41, 95% confidence interval = [1.25, 1.59], p < 0.001; odds ratio 1.60, 95% confidence interval = [1.32, 1.92], p < 0.001). Past-year deliberate self-harm was largely stable. Declines in mental health were unevenly spread and were generally greater among those with higher need in 2012 (females, Māori and Pacific students and those from higher deprivation neighbourhoods), increasing inequity, and among Asian students. Conclusion: Adolescent mental health needs are high in New Zealand and have increased sharply from 2012 among all demographic groups, especially females, Māori, Pacific and Asian students and those from high-deprivation neighbourhoods. Ethnic and socioeconomic disparities have widened.