Color blindness (color vision deficiency) is a disorder that impairs the true perception of colors. Using the information in this study, appropriate policy can be made to identify high-risk groups, as well as educational policies for families to perform more effective genetic diagnosis methods. This study aims to examine the prevalence of color blindness in Iranian students through a meta-analysis. Articles related to color blindness published between January 1990 and December 2020 were searched in Scopus, Cochrane Library, Web of Science (WoS), Science Direct, Embase, SID, MagIran, IranDoc, Medline, and Google Scholar databases. The keywords used were based on medical subject topics (MeSH Terms) and, after careful review, articles were selected according to varied sections of Participants, Exposure, Comparison, and Outcomes (PECO). Participants: students; Exposure: students with color blindness were examined; Comparison: Students from multiple provinces and regions of Iran were surveyed for color blindness; Outcomes: the pooled prevalence of color blindness in Iranian students reported from different provinces. The prevalence of color blindness in Iranian students was 3.8% (95% CI: 2.7–5.4%). The pooled prevalence of color blindness in Iranian male and female students was 4.7% (95% CI: 3.5–6.4%) and 0.7% (95% CI: 0.3–1.3%), respectively. The pooled prevalence of red–green color blindness (Tritan) was 41.7% (95% CI: 18.9–68.8%). The pooled prevalence of red color blindness (Protan) was 13.9% (95% CI: 7.8–23.8%), and the pooled prevalence of green color blindness (Deutan) based on meta-analysis was 45.3% (95% CI: 29–62.7%). Due to the high prevalence of color blindness in students, especially male students, it is necessary to be screened for through genetic tests in couples before having children.