This study explores the perception of social and educational quality of life in minors with rare diseases (RDs). Two meta-analyses were performed, applying the random effects model. Results: Regarding the social Quality of Life, the meta-sample consisted of k = 40 samples, with a total population of 1943 children (mean age = 9.42 years), of whom 687 (35.3%) were girls, 615 (31.4%) were boys and 641 (33%) did not report their sex. The effect size was large (mean size = 7.68; p < 0.000; 99% Confidence Interval; lower limit = 7.22; upper limit = 8.14). The results of the meta-regression and model analysis showed the importance of the measurement instrument (Paediatric Quality-of-Life Inventory and Prototypes of the Quality of life) and the dissimilarity of perception among caregivers. The nationality and the type of RD were not relevant. With respect to the educational Quality of Life, the meta-sample consisted of k = 19 samples, with 699 minors (mean age = 10.3 years), of whom 266 (38%) were girls, 242 (34.6%) were boys and 191 (27.4%) did not report their sex. The effect size was large (mean size = 7.15; p < 0.000; 99% CI; lower limit = 6.35; upper limit = 7.94). The meta-regression and comparison of models showed that the type of RD was essential. The measurement instrument was a moderating variable, especially the Parent version Paediatric Quality-of-Life Inventory. This study reveals the need for further research on RDs and their social-educational effects.