Anxiety and depression are prevalent among university students and many universities offer psychological services to assist students. Unfortunately, students can experience barriers that prevent access to these services and many university services experience difficulties meeting demand. The present pragmatic randomised controlled trial examined the preliminary efficacy and acceptability of a transdiagnostic and internet-delivered cognitive behavioural therapy (CBT) programme for university students seeking help with anxiety and depression. Participants were randomly allocated to either a treatment group (n = 30) or a waitlist-control group (n = 23). The treatment group received weekly contact with a therapist, via telephone or a secure messaging system, as well as automated emails that guided their progress through the programme. Significant reductions were found on standard measures of anxiety (Cohen's d = 0.66; 95% CI: 0.13 to 1.17) and depression (Cohen's d = 0.81; 95% CI: 0.27 to 1.32) among the treatment group participants, but no significant differences were found between the treatment and control groups at post-treatment. However, more pronounced reductions were found among treatment group participants with clinical level symptoms of anxiety (Cohen's d = 1.33; 95% CI: 0.62 to 1.99) and depression (Cohen's d = 1.59; 95% CI: 0.81 to 2.30), who reported significantly lower levels of symptoms than control group participants at post-treatment. These reductions were maintained at 3-month follow-up and participants rated the intervention as acceptable. The results provide preliminary support for the potential of iCBT for university students with anxiety and depression. However, larger scale implementation trials considering a broader range of outcomes are required.