Modeling using simulations is a promising approach for integrating programming into science education. In this paper we use the technological pedagogical and content knowledge (TPACK) framework developed by Mishra and Koehler (2006) to examine and develop pre-service teachers’ (PSTs’) knowledge of integrating computational thinking into science education in the context of programming simulations in Scratch. We have used design-based research to develop a learning sequence for PSTs concerning this topic. Through two iterations we explored how the learning sequence contributed to developing PSTs’ TPACK. We investigated PSTs’ learning processes when they designed lesson plans for teaching programming of simulations in science education aimed at the lower secondary level. Our results suggest that PSTs’ TPACK developed when creating lesson plans fitted to simulations created during the learning sequence. In addition, we found that PSTs shifted their focus from the programming content to the science content when we made the inquiry and modeling elements more explicit during the programming. Based on this, we propose design principles for developing PSTs’ TPACK related to the programming of simulations of science phenomena.