Objectives: Neonatal mortality is a global public health problem. The efforts to reduce child mortality are one of the 2030 Agenda for Sustainable Development goals. The availability of neonatal mortality rates (NMR) data in Brazilian health facilities is crucial to understanding the dynamic, identify gaps, and provide information to allocate resources and actions to reduce NMR at the health facility level. The objective is to offer an integrated dataset containing monthly data in a historical series from 2007 to 2017 with information on all births, neonatal deaths, and NMR (total, early, and late components) enriched with the municipality’s information. Data description: Dataset with historical data with information on the number of births, the neonatal deaths, the neonatal mortality rate (including early and late components), and geographic information for each health facility in Brazil, comprising the years between 2005 and 2017.