Maternal nutrition during pregnancy is an important intrauterine environmental factor associated with potential disease risk in later life. In this study, we investigated how epigenetic regulation of the muscle glucose transporter GLUT4 is modified in the offspring. Timed‐pregnant Sprague Dawley rats were fed with one of two isocaloric diets, control (18% casein) or low protein diet (9% casein) during gestation period. At birth, all mothers received a standardized meal ad libitum. The skeletal muscle was removed when pups were 38 days old. GLUT4 mRNA expression in female rat skeletal muscle was increased significantly by maternal low protein diet. An increase of expression in genes associated with glucose metabolism, such as CEBPβ and Nur77, was observed in female pups whose mothers were fed with low protein diet. Employing ChIP, we observed that modifications of histone acetylation and methylation at GLUT4 promoter region in female pup muscle were linked with the alteration in GLUT4 expression. However, the increased GLUT4 expression was not mediated by amino acid response pathway or DNA demethylation. These results suggest that a maternal diet limited in protein epigenetically alters fetal chromatin via covalent modifications of histones and subsequently alters gene‐specific expression.