(1) Background: The aim of this study is to investigate the effects of internet-based intervention programs for reducing stress, anxiety, and depression among university students during the COVID-19 pandemic by conducting a meta-analysis. (2) Methods: Searches were conducted in the following databases: MEDLINE, EbscoHost Academic Search Ultimate, and PsycArticles, using a combination of “Covid-19 AND ‘Randomized Controlled Trial’ AND students”, as well as a combination of the following search terms: “internet”, “online”, “treat_”, “psycholog_”, “intervention”, “program_”, “stress_”, “depress_”, “anxiety”, “university”, “college”, ”freshm_”, “sophomore_”, and “undergraduat_”. The population, intervention, control, outcomes, and study design (PICOS) framework was used (P (population): university students during the COVID-19 pandemic; I (intervention): internet-based intervention programs for reducing stress, anxiety, and depression; C (control): no intervention, usual care, or on a waiting list; O (outcomes): stress, anxiety, and depression indicators; S (study design): meta-analysis including only randomized controlled trials (RCTs)). A meta-analysis was performed on the 10 retrieved studies published between 2021 and 2022. Only RCTs were analyzed. (3) Results: All 10 analyzed papers revealed a trend in the effectiveness of internet-based intervention for reducing stress, anxiety, and depression in university students during COVID-19. Significant effects from the included RCTs with interventions for reducing stress and depression were established. (4) Conclusions: Psychological internet-based interventions may help to reduce depression and stress among university students; however, more research is needed to determine their effectiveness in reducing anxiety.