Introduction There are now nearly 50 000 children with a life-limiting or life-threatening condition in the UK. These include conditions where there is no reasonable hope of cure and from which they will die, as well as conditions for which curative treatment may be feasible but can fail, for example, cancer or heart failure. Having a child with a life-limiting condition involves being a coordinator and provider of healthcare in addition to the responsibilities and pressures of parenting a child who is expected to die young. This adversely affects the health and well-being of these mothers and affects their ability to care for their child, but the extent of the impact is poorly understood. This study aims to quantify the incidence and nature of mental and physical morbidity in mothers of children with a life-limiting condition, their healthcare use and to assess whether there is a relationship between the health of the mother and the child’s condition. Methods and analysis A comparative cohort study using data from the Clinical Practice Research Datalink and linked hospital data will include three groups of children and their mothers (those with a life-limiting condition, those with a chronic condition and those with no long-term health condition total=20 000 mother–child dyads). Incidence rates and incidence rate ratios will be used to quantify and compare the outcomes between groups with multivariable regression modelling used to assess the relationship between the child’s disease trajectory and mother’s health. Ethics and dissemination This study protocol has approval from the Independent Scientific Advisory Committee for the UK Medicines and Healthcare products Regulatory Agency Database Research. The results of this study will be reported according to the STROBE and RECORD guidelines. There will also be a lay summary for parents which will be available to download from the Martin House Research Centre website (www.york.ac.uk/mhrc).