The coronavirus disease 2019 (COVID-19) pandemic has influenced all aspects significantly, and an estimated 1.5 billion students across the globe have been forced to keep up with online courses at home. Many recent empirical studies reported the prevalence of mental health problems among students caused by remote learning during the COVID-19 pandemic, but a few studies aggregated these results. Therefore, to strengthen statistical power, the article aimed to examine the prevalence of anxiety, depression, and stress among remote learning students during the COVID-19 pandemic via a meta-analysis. A total of 36 original articles have been selected from five academic databases, including Web of Science, PubMed, Scopus, EBSCO, and Google Scholar, covering 78,674 participants in 19 nations, and yielding 60 effect sizes (22 for anxiety, 17 for depression, and 21 for stress) based on the random effects model via Comprehensive Meta-Analysis (CMA) software. The results showed that the prevalence of anxiety, depression, and stress among remote learning students during the COVID-19 pandemic was as high as 58, 50, and 71%, respectively. Besides, the moderator analysis found that (1) the prevalence of anxiety and depression among students in higher education was significantly higher than that of students in elementary education. (2) an increasing number of medical students and students in emergency remote learning context suffered from mental stress than their non-medical and traditional distance learning counterparts. Thus, the COVID-19 pandemic triggers concerns related to physical health and mental disorders, especially for remote online learning students. The current situation should be brought to the forefront by educators to develop psychological interventions for relieving students’ anxiety, depression, and stress during the pandemic period.