Climate change and its impact on the agricultural sector represent one of the most important challenges in terms of adaptation, particularly in the field of animal production. To understand the molecular mechanisms underlying the response of hens to heat exposure, the aim of this study was to compare DNA methylation profiles in offspring whose mothers had or had not been exposed to a heat-stressed environment. All animals were reared at 22 °C until 28 weeks of age. Between 28 and 32 weeks of age, half the hens were kept at 32 °C. Eggs were collected between 31 and 32 weeks of age. Sequencing data from a reduced representation of the genome treated with sodium bisulfite, allowing analysis of cytosine methylation, were obtained on the whole brains of 22 embryos at 13 days of age, from both heat-stressed and non-heat-stressed hens. We detected 289 differentially methylated cytosines (DMC) between the offspring of heat-stressed mothers and controls. These DMCs are associated with 357 genes, which play an important role in processes such as development and cellular response to stimulus. This study provides valuable information on the adaptive mechanisms involved in the response of embryos to their mother’s heat exposition: heat exposition in hens can lead to changes in the methylation profiles of offspring during the embryonic stage, which may influence their response to subsequent heatwave exposures.