Introduction: Approximately 14% of Australian women smoke during pregnancy. Although the risk of adverse outcomes is reduced by smoking cessation, less than 35% of Australian women quit smoking spontaneously during pregnancy. Evidence for the efficacy of bupropion, varenicline or nicotine replacement therapy as smoking cessation aids in the non-pregnant population suggest that pharmacotherapy for smoking cessation is worth exploring in women of childbearing age. Currently, little is known about the utilisation, effectiveness and safety of pharmacotherapies for smoking cessation during pregnancy; neither the extent to which they are used prior to pregnancy nor whether their use has changed in response to related policy reforms. The Smoking MUMS (Maternal Use of Medications and Safety) Study will explore these issues using linked person-level data for a population-based cohort of Australian mothers. Methods and analysis: The cohort will be assembled by linking administrative health records for all women who gave birth in New South Wales or Western Australia since 2003 and their children, including records relating to childbirth, use of pharmaceuticals, hospital admissions, emergency department presentations and deaths. These longitudinal linked data will be used to identify utilisation of smoking cessation pharmacotherapies during and between pregnancies and to explore the associated smoking cessation rates and maternal and child health outcomes. Subgroup and temporal analyses will identify potential differences between population groups including indigenous mothers and social security recipients and track changes associated with policy reforms that have made alternative smoking cessation pharmacotherapies available. Ethics and dissemination: Ethical approval has been obtained for this study. To enhance the translation of the project's findings into policy and practice, policy and clinical stakeholders will be engaged through a reference group and a policy forum will be held. Outputs from the project will include scientific papers and summary reports designed for policy audiences.