Background <p>Secondary schools are increasingly delivering a range of mental health interventions with varied success. This trial examined the effectiveness of two implementation strategies, allocation of class time and provision of financial incentives, on the engagement of secondary students with a universal web-based mental health service, <i>Smooth Sailing</i>.</p> Methods <p>A three-arm, cluster-randomised trial was conducted over 12&#xa0;weeks with Grade 8 and 9 students from 20 schools in two Australian states. Schools were randomised to: (1) the standard <i>Smooth Sailing</i> service, (2) the standard service plus extra class time, or (3) the standard service plus financial incentives. The primary outcome was student engagement, measured by the number of modules accessed at 12-weeks post-baseline. Secondary outcomes included uptake, retention, help-seeking intentions for mental health problems, service satisfaction, and barriers to use.</p> Results <p>A total of 20 schools consented, and 1295 students participated. Students accessed a higher number of modules in the enhanced conditions compared with the standard service, but the differences were not statistically significant (<i>p</i> = 0.14). There were no significant differences in uptake (<i>p</i> = 0.55) or retention (<i>p</i> = 0.95) between conditions. Help-seeking intentions significantly improved at 6- and 12-weeks in the standard service and class time conditions only. Common barriers to service use among students were forgetfulness and low motivation.</p> Conclusions <p>Neither class time allocation nor financial incentives significantly increased student engagement, as measured by modules accessed, highlighting the challenges of optimising engagement with digital mental health services in schools and emphasising the need to consider the broader school context.</p> <p><i>Trial registration</i> Australian New Zealand Clinical Trial Registry (ACTRN12621000225819) and Universal Trial Number (U1111-1265-7440).</p>