Children have been identified as being particularly vulnerable to energy poverty (EP), but little empirical research has addressed the effect of EP on children’s health and wellbeing, especially in southern Europe. In this work we aimed to provide an in-depth description of the distribution of EP by sociodemographic, socioeconomic and housing characteristics, as well as to analyse the association between EP and health and wellbeing in children in Barcelona. We performed a cross-sectional study using data from the Barcelona Health Survey for 2016 (n = 481 children under 15 years). We analysed the association between EP and health outcomes through prevalence differences and prevalence ratios (PR) and their 95% confidence interval (CI), using Poisson regression models with robust variance. In Barcelona, 10.6% of children were living in EP and large inequalities were found by sociodemographic, socioeconomic and housing characteristics. EP was strongly associated with poor health in children (PR (95% CI): 7.70 (2.86, 20.72)). Living in EP was also associated with poor mental health (PR (95% CI): 2.46 (1.21, 4.99)) and with more cases of asthma (PR (95% CI): 4.19 (1.47, 11.90)) and overweight (PR (95% CI): 1.50 (1.05, 2.15)) in children. It is urgent to develop specific measures to avoid such serious and unfair health effects on children.