Objective To assess if the overall utilisation of surgery in Danish children 0–5 years of age increased in the period 1999–2018 in line with the development within specialised medical services. The epidemiology on surgical procedures is scarce. Methods National register-based cohort study of all Danish children born 1994–2018 (n = 1,599,573) using data on surgery in public and private hospitals from The National Patient Register and data on surgery in private specialist practice from The Health Service Register. Incidence rate ratios were calculated using Poisson regression with 1999 as the reference year. Results During the study period 115,573 different children (7.2% of the cohort) underwent surgery. The overall incidence of surgical procedures was stable, but the use of surgery increased in neonates mainly due to an increase in frenectomy. Boys underwent more surgery than girls. In children with severe chronic disease the rate of surgery decreased in public hospitals and increased in private specialist practices. Conclusion The utilisation of surgical procedures in Danish children 0–5 years of age did not increase from 1999 to 2018. The use of available register data in the present study may inspire surgeons to conduct further studies to enhance the knowledge within the area of surgical procedures.