Aims Becker muscular dystrophy (BMD) and Duchenne muscular dystrophy (DMD) are associated with intelligence quotients (IQs) lower than the normative values, and it is suggested that IQ is negatively correlated with the number of affected isoforms (i.e., Dp427, Dp140 and Dp71). Therefore, the objective of this meta‐analysis was to estimate the IQ, and the IQ–genotype association according to the altered dystrophin isoforms, in the population with BMD or DMD. Methods A systematic search in Medline, Web of Science, Scopus and the Cochrane Library was conducted from inception to March 2023. Observational studies that determined the IQ and/or the IQ by genotype in the population with BMD or DMD were included. Meta‐analyses of IQ, IQ by genotype and IQ–genotype association by comparing IQ according to the genotype were conducted. The results are shown as the mean/mean differences and 95% confidence intervals. Results Fifty‐one studies were included. The IQ in BMD was 89.92 (85.84, 94.01) and in DMD was 84.61 (82.97, 86.26). Moreover, the IQ for Dp427−/Dp140+/Dp71+ and Dp427−/Dp140−/Dp71+ was 90.62 (86.72, 94.53) and 80.73 (67.49, 93.98) in BMD, while the IQ for Dp427−/Dp140+/Dp71+, Dp427−/Dp140−/Dp71+ and Dp427−/Dp140−/Dp71− was 93.05 (89.42, 96.67), 81.78 (77.23, 86.32) and 49.19 (40.47, 57.90) in DMD. Finally, in DMD, Dp427−/Dp140−/Dp71+ vs Dp427−/Dp140+/Dp71+ and Dp427−/Dp140−/Dp71− vs Dp427−/Dp140−/Dp71+ were associated with −10.73 (−14.66, −6.81) and −36.14 (−48.87, −23.41) points, respectively. Conclusions The IQ in BMD and DMD was lower than the normative values. Moreover, in DMD, there is a synergistic association between the number of affected isoforms and IQ.