Objectives Delayed vaccination in children with seizures was common in China. This study aims to describe the vaccination status, reasons for vaccination deferral, vaccination recommendations and the safety for these patients in Zhejiang. Methods 1539 children included were divided into febrile seizure (FS) group, epilepsy (EP) group, unclassified seizure group and other symptomatic seizure group. The medical records and reasons for the vaccination deferral were collected by questionnaire. Vaccination data and Adverse Event Following Immunization (AEFI) were retrieved from the vaccination booklets. Results The main diseases of the children enrolled were FS (756, 49.1%) and EP (443, 28.8%). Most of them (95.6%) were vaccinated on time before the onset of seizure, but their vaccination was delayed after seizure occurred. 76.1% were recommended to receive vaccines normally, of which the FS group accounted for the highest proportion (90.3%). 88.73% of them were vaccinated as recommended, and there were no serious side effects or seizure reoccurrence. The main reason for vaccination deferral was providers’ and parents’ hesitation to have these children vaccinated. Conclusion Seizures were overestimated as a contraindication for vaccination in China. Routine vaccination was safe in most circumstances. It is essential to educate providers and parents about the benefits and contraindications of vaccination in children with seizures.