Background X-linked red-green color blindness is the most widespread form of vision impairment. The study aimed to determine the prevalence and allele frequencies of red-green color vision impairments among school children in Repi primary school in Addis Ababa, Ethiopia. Methods A cross-sectional survey was employed involving 2400 healthy subjects (females = 850 and males = 1550) in in Repi primary school. The Ishihara pseudo-isochromatic 24 plate edition was used to test the colour vision of students under natural day light condition. Results The prevalence of congenial colour vision deficiency (CCVD) was 2.29%; 50 (3.23%) males and 5 (0.56%) females were affected with CCVD. The frequencies of achromacy, deutan and protan in male subjects were 0.13%, 1.75%, and 0.50%, respectively. Both Deutan and protan were highest among students of Amhara ethnic origin 2.85 % and 1.08%, respectively. Conclusions The overall prevalence of CCVD found in the present study was lower compared to the previous studies done in Ethiopia. There was clear variation in the prevalence of color vision deficiency among students of various ethnic groups. Proper screening, education and counseling are needed to minimize impacts of CCVD in the country, and can also be beneficial for the affected subject in tackling difficulties in everyday work and for proper choice of future profession.