Azathioprine is a first‐line drug used to maintain the remission of inflammatory bowel disease (IBD). As a prodrug, azathioprine is metabolised to produce active 6‐thioguanine nucleotides (6‐TGN). There are large individual variations in the pharmacokinetics/pharmacodynamics of 6‐TGN in patients with IBD. Here, we aimed to develop a model to quantitatively investigate factors that affect 6‐TGN pharmacokinetics to formulate a dosage guideline for azathioprine. Data were collected prospectively from 100 adult patients with IBD who were receiving azathioprine. Patients were genotyped for two single‐nucleotide polymorphisms (TPMT*3C c.719A > G and NUDT15 c.415C > T). Using high‐performance liquid chromatography, we measured 156 steady‐state trough concentrations of 6‐TGN within the range 0.09 to 1.16 mg/L (ie 133‐1733 pmol per 8 × 108 RBC). The covariates analysed included sex, age, body‐weight, laboratory tests and concomitant medications. A population pharmacokinetic model was established using "non‐linear mixed‐effects modelling" software and the "first‐order conditional estimation method with interaction." Body‐weight, TPMT*3C polymorphisms and co‐therapy with mesalazine were found to be important factors influencing the clearance of 6‐TGN. A dosage guideline for azathioprine was developed based on the PPK model that enables individualised azathioprine dosing in adult patients with different body‐weights, TPMT*3C genotypes and co‐administration with mesalazine. [ABSTRACT FROM AUTHOR]