Renewable energy plays an essential role for the challenges that bring climate change. Enhancing clean technology innovation performance, supported by patent applications, is a fundamental way to contribute to the emission reduction. Exploring the patent applications contribute to reveal opportunities and challenges in the energy sector. Thus, this paper discusses the impact of the patent application delays on the incentives for innovation which contribute to the clean energy transition. To understand the impacts on the long-term, this paper proposes a simulation model based on system dynamics modelling. Results show that the delays of patent applications could have a significant impact on the clean energy transition in Latin America.