Internet-based cognitive behavioral interventions (iCBTs) are efficacious treatments for depression and anxiety. However, it is unknown whether adding human guidance is feasible and beneficial within a large educational setting. This study aims to potentially demonstrate the superiority of 2 variants of a transdiagnostic iCBT program (human-guided and computer-guided iCBT) over care as usual (CAU) in a large sample of university students and the superiority of human-guided iCBT over computer-guided iCBT. A total of 801 students with elevated levels of anxiety, depression, or both from a large university in the Netherlands were recruited as participants and randomized to 1 of 3 conditions: human-guided iCBT, computer-guided iCBT, and CAU. The primary outcome measures were depression (Patient Health Questionnaire) and anxiety (Generalized Anxiety Disorder scale). Secondary outcomes included substance use-related problems (Alcohol Use Disorder Identification Test and Drug Abuse Screening Test-10 items). Linear mixed models were used to estimate the effects of time, treatment group, and their interactions (slopes). The primary research question was whether the 3 conditions differed in improvement over 3 time points (baseline, midtreatment, and after treatment) in terms of depression and anxiety symptoms. Results were analyzed according to the intention-to-treat principle using multiple imputation. Patients were followed exploratively from baseline to 6 and 12 months. In both short-term and long-term analyses, the slopes for the 3 conditions did not differ significantly in terms of depression and anxiety, although both web-based interventions were marginally more efficacious than CAU over 6 months (P values between .02 and .03). All groups showed significant improvement over time (P<.001). For the secondary outcomes, only significant improvements over time (across and not between groups) were found for drug use (P<.001). Significant differences were found in terms of adherence, indicating that participants in the human-guided condition did more sessions than those in the computer-guided condition (P=.002). The transdiagnostic iCBT program offers a practical, feasible, and efficacious alternative to usual care to tackle mental health problems in a large university setting. There is no indication that human guidance should be preferred over technological guidance. The potential preference of human support also depends on the scale of implementation and cost-effectiveness, which need to be addressed in future trials. International Clinical Trials Registry Platform NL7328/NTR7544; https://trialsearch.who.int/Trial2.aspx?TrialID=NL-OMON26795.