For computer simulations of physiological experiments by physiological models, a machine-readable description of experimental protocols is useful. Although description formats for cell physiological models are already available, there is no specialized representation format for experimental protocols. Here, we propose an XML-based language, PEPML (Physiological Experimental Protocol Markup Language), and a simulation method of experimental protocols in PEPML. In the PEPML, conditions and procedures of an experimental protocol are procedurally described as a list of events, each of which consists of a condition for execution and an action to be executed. By specifying the references of variables in a protocol using an ontology, the protocol can be applied to various models without editing tasks. The proposed simulation method allows unambiguous numerical calculation of a procedural experimental protocol, which is applied to a declaratively represented model by interpretation of the protocol as a set of boundary conditions for the model variables. PEPML and the proposed method allow applying both multiple protocols to a single model and a single protocol to multiple models. This feature facilitates the efficient simulation for verification, comparison and utilization of physiological models.