The Brazilian Automotive and Aeronautic Industries are both important sectors for the National Innovation System. Through this research, we aim to understand the Innovation System of both sectors in order to collect lessons learned for the Automotive Industry Innovation Policy called Inovar-Auto (Innovate-Auto), which was effective from the beginning of 2013 until the end of 2017. This study was conducted based on the quantitative analysis of sectoral investment in R&D and the number of patents as well as on the qualitative analysis of some critical projects performed by companies in both industry sectors, the Automotive and the Aeronautic. All data were collected via interviews with the agents of the sectoral innovation system. This article aims to contribute to the analysis of a sectoral innovation system based on an analytical tool to measure the maturity level on specific key variables.