Introduction Waiting to start treatment has been shown to be associated with tumor progression and upstaging in head and neck squamous cell carcinomas (HNSCCs). This diminishes the chance of cure and might lead to unnecessary mortality. We investigated the association between waiting times and survival in the Netherlands and assessed which factors were associated to longer waiting times. Methods Patient (age, sex, socioeconomic status (SES), tumor (site, stage) and treatment (type, of institute of diagnosis/treatment) characteristics for patients with HNSCC who underwent treatment were extracted from the Netherlands Cancer Registry (NCR) for 2005–2011. Waiting time was defined as the number of days between histopathological diagnosis and start of treatment. Univariable and multivariable Cox regression was used to evaluate survival. Results In total, 13,140 patients were included, who had a median waiting time of 37 days. Patients who were more likely to wait longer were men, patients with a low SES, oropharynx tumors, stage IV tumors, patients to be treated with radiotherapy or chemoradiation, and patients referred for treatment to a Head and Neck Oncology Center (HNOC) from another hospital. The 5-year overall survival was 58% for all patients. Our multivariable Cox regression model showed that longer waiting time, was significantly related to a higher hazard of dying ( p < 0.0001). Conclusion This is the first large population-based study showing that longer waiting time for surgery, radiotherapy or chemoradiation is a significant negative prognostic factor for HNSCC patients.