Abstract Background Studies indicate unwarranted variation in a wide range of neonatal care practices, contributing to preventable morbidity and mortality. Unwarranted variation is the result of complex interactions and multiple determinants. One of the determinants contributing to unwarranted variation in care may be variation in local hospital protocols. The purpose of this study was to examine variation in the content of obstetric and neonatal protocols for six common indications for neonatal referral to the pediatrician: large for gestational age/macrosomia, small for gestational age/fetal growth restriction, meconium‐stained amniotic fluid, vacuum extraction, forceps extraction, and cesarean birth. Methods We conducted a nationwide cross‐sectional study examining protocols for neonatal referral to the pediatrician in the obstetric and neonatal departments of all Dutch hospitals. Variation in protocols was analyzed between regions, between neonatal and obstetrics departments located in the same hospital, and within neonatal and obstetrics departments. Results There was considerable variation in protocols between regions, between neonatal and obstetrics departments, and within neonatal and obstetrics departments. The results of this study showed considerable variation in recommendations for type of referral, admission, screening/diagnostic tests, treatment, and discharge. Furthermore, results generally showed lower referral thresholds in neonatal departments compared with obstetric departments, and higher referral thresholds in the eastern region of the Netherlands. We also found variation in local hospital protocols, which could not be explained by population characteristics but which may be explained by varying recommendations in existing national and international guidelines and/or lack of adherence to these guidelines. Conclusions To reduce unwarranted variation in local protocols, evidence‐based, multidisciplinary guidelines should be developed in the Netherlands. Further research addressing knowledge ...