Background Oral and oropharyngeal cancers are considered an important public health problem around all world. The most effective way to improve survival and reduce disease-related morbidity and mortality is the prevention of its major risk factors combined with early detection. This study aims to analyze the association between late diagnosis of oral and oropharyngeal cancers in Brazil and the contextual socioeconomic and coverage indicators of Primary Health Care (PHC), as well as to assess the temporal trend of the late diagnosis. Methods This observational study evaluated secondary data with a time series analysis. All Brazilian cities that reported at least one case of oral and oropharyngeal cancers each year, between 2000 and 2013 were included. These data were obtained from the National Cancer Institute José Alencar Gomes da Silva (INCA); the staging was analyzed by calculating the ratio risk for late diagnosis by municipality. The association between staging and socioeconomic variables and PHC provision was calculated using multiple linear regression. The time trend of the risk ratio for late-stage diagnosis was calculated using the Prais-Winsten method. Results One hundred and sixty Brazilian municipalities had at least one annual case of oral and oropharyngeal cancers notified to the INCA hospital system between 2000 and 2013. The adjusted model identified that the higher the Gini value (greater social inequality) and the lower the HDI value (less human development), the greater the number of tumors diagnosed at a late stage, considering the size of the tumor. A greater risk for late diagnosis was identified, already in the stage of lymph node involvement, when there is greater social inequality and less coverage of Oral Health Team (OHT) in PHC. The greater the social inequality, the greater the risk of late diagnosis, already in the metastasis stage. Conclusions Better socioeconomic indicators and greater coverage by the OHT were associated with the diagnosis of oral and oropharyngeal cancers still in the early stages. During the evaluated period, there was an increase in the number of cases diagnosed at the most advanced stage.