Simulink is a de-facto industrial standard for embedded system design. In previous work, we developed a compositional analysis framework for Simulink, the Refinement Calculus of Reactive Systems (RCRS), which allows checking compatibility and substitutability of components. However, standard type checking was not considered in that work. In this paper we present a method for the type inference of Simulink models using the Isabelle theorem prover. A Simulink diagram is translated into an (RCRS) Isabelle theory. Then Isabelle’s powerful type inference mechanism is used to infer the types of the diagram based on the types of the basic blocks. One of the aims is to handle formally as many diagrams as possible. In particular, we want to be able to handle even those diagrams that may have typing ambiguities, provided that they are accepted by Simulink. This method is implemented in our toolset that translates Simulink diagrams into Isabelle theories and simplifies them. We evaluate our technique on several case studies, most notably, an automotive fuel control system benchmark provided by Toyota.