Anti‐tumour necrosis factor (anti‐TNF agents) are widely applied for IBD (Inflammatory bowel disease) patients; however, the timing of the last dosing for IBD pregnancy and time to elimination in anti‐TNF agent‐exposed infants is controversial. This study aimed to determine the optimal timing for the last dosing of anti‐TNF agents (infliximab, adalimumab, and golimumab) in pregnant women with IBD, as well as to investigate the recommended vaccine schedules for infants exposed to these drugs. A physiologically based pharmacokinetic (PBPK) model of anti‐TNF agents was built for adults and extrapolated to pregnant patients, foetuses, and infants. The PBPK models successfully predicted and verified the pharmacokinetics of infliximab, adalimumab, and golimumab in pregnancy, foetuses, and infants. The predicted pharmacokinetic data were within two‐fold of the observed data. The simulated results were used as timing advice. According to the dose of administration, the suggested timing of the last dosing for infliximab, adalimumab, and golimumab is successfully provided based on PBPK predictions. PBPK models indicated that for infants, the advocated timing of vaccination is 12 months, 8 months, and 5 months after birth for infliximab, adalimumab, and golimumab, respectively. Our study illustrated that PBPK models can provide a valuable tool to predict the pharmacokinetics of large macromolecules in pregnant women, foetuses, and infants, ultimately informing drug‐treatment decisions for pregnancy and vaccination regimens for infants.