Some children have disproportional difficulties in understanding what they read. These children frequently have underlying oral language problems, yet typically go unnoticed in the classroom (Nation et al., 2004). While we know that children with reading accuracy difficulties are at risk for low educational attainment and poor mental health, studies of comprehension problems are scarce and small-scale in nature. We addressed this gap using data from the Avon Longitudinal Study of Parents and Children (ALSPAC). Children with comprehension weaknesses (n = 947) were identified using a latent profile analysis on reading and language measures at age 8-9 years (James et al., 2023). These children typically had poorer vocabulary and nonverbal IQ than peers without reading difficulties. We conducted two further preregistered studies to examine (1) their likelihood of meeting national educational targets in English, Maths, and Science assessments at ages 11 and 14 years (Stage 1 IPA; https://osf.io/th9qw); and (2) the prevalence of internalising and externalising behaviours at ages 9, 11, and 13 years, as measured by the Strengths and Difficulties Questionnaire (https://osf.io/ztr97). Both studies analysed outcomes using mixed effects models. The odds of children with comprehension weaknesses meeting or exceeding educational targets were 58% lower than for peers without reading difficulties, and comparable to those with reading accuracy weaknesses. These educational difficulties were more marked in Maths and Science than in English assessments, remained consistent over time, and typically withstood controlling for sociodemographic factors. However, there was no indication that problems were accompanied by increased rates of internalising or externalising behaviours. The findings reinforce the message that good reading accuracy is not sufficient for educational success, and that children with poor language comprehension may need broad support across the curriculum. However, there is no indication as yet that this support needs to routinely target wellbeing in early adolescence.