Background The study was performed to determine the epidemiological, clinical, and histopathological characteristics and prognosis of primary mucosal melanoma of the head and neck (MMHN) in Denmark. Material and methods This was a national retrospective multicenter study of patients diagnosed with MMHN between 1982 and 2012 in Denmark. Data were retrieved from national databases and patient records. Incidence trends were examined for the entire period. We prepared survival curves and performed univariate and multivariate analysis for the period 1992-2012 to identify possible prognostic factors. Results No significant trends in incidence were found in the study period. The three-year overall and disease-free survival rates for MMHN were 46.5% and 35.5%, respectively. Negative margins was an independent predictor of disease-free survival, and age below 65, absence of distant metastases, and low overall TNM stage were predictors of overall survival. Radiotherapy did not improve survival significantly. Recurrence rates were high, even for patients with negative margins. Conclusions MMHN remains a rare disease with a poor prognosis, particularly for patients aged over 65, those with distant metastasis, and those with advanced TNM stage. Importantly, the rate of recurrence is lowest in patients with negative margins.