Background Current knowledge on the prevalence of asthma is mainly based on cross‐sectional questionnaire data. Current population‐based data on the incidence of asthma in children are scarce. Objective To study the incidence, prevalence, and age at diagnosis of asthma in children in the Netherlands over the study period 2000–2012. Methods A population‐based cohort study was conducted in the Integrated Primary Care Information database. The cohort consisted of 176,516 children (379,536 personyears (PY) of follow‐up), aged 5–18 years between 2000 and 2012. All medical records of children with physician diagnosed asthma were validated. Incidence rates, annual percent change (APC), and prevalence for asthma were calculated. Influence of age and gender on incidence rates and change in age at diagnosis were studied. Results We identified an asthma cohort of 14,303 children with 35,118 PY. The overall incidence rate was 6.7/1000 PY (95% CI, 6.45–6.97). Until 2008, the incidence rate was significantly increasing (APC 5.79 (95% CI 1.43–10.34); from 2008 onwards, a non‐significant decrease was observed (APC −12.16 (95% CI −23.07 to 0.28). Incidence for girls was lower than for boys, this difference decreased with increasing age. (p < 0.001) Overall, the age at diagnosis increased over calendar time and was lower for boys. (linear trend p < 0.001). Conclusion Our population‐based cohort study observed an incidence rate of 6.7 per 1000 PY of physician‐diagnosed asthma in children in the Netherlands over 2000–2012. The asthma incidence rate was increasing until 2008. Further studies are needed to confirm the decrease in asthma incidence rate from 2008 onwards.