Scientists use models to represent their imagination and conceptualization of a particular phenomenon. They then use models to develop an argument to debate, defend, and debunk ideas in their peer community. Modeling is an essential practice of authentic science. To foster the pedagogical practice of incorporating models in argumentative contexts, we introduce an approach called “Science Negotiation Pedagogy.” We show how models can support argumentation practices in science classrooms in six phases of action: (1) create a driving question; (2) construct a tentative model in groups; (3) construct a tentative argument in groups; (4) negotiate models and arguments in a whole-class discussion, then revise models and arguments through negotiation; (5) consult the experts; and (6) reflect through writing. A unit on the human respiratory system is used as an example to demonstrate how Science Negotiation Pedagogy can be implemented in biology classrooms.