Methotrexate is an antimetabolite and antifolate drug that is widely used in the treatment of malignancies and auto-immune disorders. In childhood acute lymphoblastic leukaemia, methotrexate is often combined with 6-mercaptopurine and both of them have been shown to be very effective for maintenance of remission. Large variability in the pharmacokinetics of methotrexate has led to increasing use of therapeutic drug monitoring in its clinical use to identify patients with high risk of toxicity and optimise clinical outcome. A physiologically based pharmacokinetic model was developed for methotrexate for oral and intravenous dosing and adults and paediatric use. The model has compartments for stomach, gut lumen, enterocyte, gut tissue, spleen, liver vascular, liver tissue, gall bladder, systemic plasma, red blood cells, kidney vascular, kidney tissue, skin, bone marrow, thymus, muscle and rest of body. A mechanistic model was also developed for the kidney to account for renal clearance of methotrexate via filtration and secretion. Variability on system and drug specific parameters was incorporated in the model to reflect observed clinical data and assuming the same pathways in adults and children, age-dependent changes in body size, organ volumes and plasma flows, the model was scaled to children. The model was developed successfully for adults and parameters such as net secretion clearance, biliary transit time and red blood cell distribution and binding parameters were estimated from published adult profiles. A relationship between fraction absorbed and dose using reported mean bioavailability data in the literature was also established. The model also incorporates non-linear binding in some tissues that has been described in the literature. Predictions using this model provide adequate description of observed plasma concentration data in adults and children. The model can be used to predict plasma and tissue concentrations of methotrexate following intravenous and oral dosing in adults and children and therefore help to improve clinical outcome.