Introduction: The survival among children with cancer has improved considerably the past decades. Consequently, more children are at risk of second primary cancers (SPC). This study aimed to investigate the incidence of SPC among pediatric head and neck cancer (HNC) patients. Methods and materials: Data on children aged 0–17 years registered with a HNC in the Danish Registry of Childhood Cancer and the Danish National Patient Registry during the period 1980–2014 was obtained. SPC was defined as registration with any second malignancy that was not simultaneous with the first primary cancer (FPC) or a relapse hereof. All information was validated through review of medical charts. Standardized incidence rates (SIR) were calculated using the average incidence of all cancers in the general population of Denmark during the study period as reference. Results: Among 234 pediatric HNC patients, six patients (four females) were registered with a SPC (2.6%), corresponding to an overall SIR of 4.8. No patients were diagnosed with more than one SPC. The median age at FPC and SPC was 15.2 years (range 9–16 years) and 35.0 years (range 19–41 years). The most common tumor histology and location among the patients with SPC was nasopharyngeal lymphoepithelial carcinoma for FPC and basal cell carcinoma of the skin for SPC. Conclusion: During 1980–2014 we identified six cases of SPC among 234 pediatric head and neck cancer patients in Denmark, corresponding to an overall SIR of 4.8.