This meta-analysis examined research on the effects of self-regulated learning scaffolds on academic performance in computer-based learning environments from 2004 to 2015. A total of 29 articles met inclusion criteria and were included in the final analysis with a total sample size of 2648 students. Moderator analyses were performed using a random effects model that focused on the three main areas of scaffold characteristics (including the mechanism, functions, delivery forms, mode, and number of scaffolds; how to promote self-regulated learning by scaffolds); demographics of the selected studies (including sample groups, sample size, learning domain, research settings, and types of computer-based learning environments); and research methodological features (including research methods, types of research design, types of organization for treatment, and duration of treatment). Findings revealed that self-regulated learning scaffolds in computer-based learning environments generally produced a significantly positive effect on academic performance (ES = 0.438). It is also suggested that both domain-general and domain-specific scaffolds can support the entire process of self-regulated learning since they demonstrated substantial effects on academic performance. Different impacts of various studies and their methodological features are presented and discussed.