After several decades of advances, simulation has become an important tool in the modeling of transportation systems and is widely applied in practice. Guides have been created by organizations in several countries, and dozens of papers have been published in scientific journals on the theory and application of transport simulation; these works are aimed at guiding practitioners in the use of simulation tools. However, transport simulation still lacks a unified and comprehensive guide for use in practice. The lack of such a document leads to conflicts between modelers, agencies, and decision makers and allows inappropriate use of the models. The outcome is often inaccurate results, inefficient use of resources, and conflict. This paper reviews and analyzes the existing transportation simulation guides. It identifies gaps and limitations and proposes an outline for a comprehensive simulation manual that is based on stakeholder input. Review of the existing guidance documents reveals that almost all these documents focus on traffic operations, and they provide either broad guidelines for building simulation models or advice on using a specific software product. Other issues, particularly those related to topics such as safety assessments, environmental impacts, public transportation, pedestrians, bicycles, simulation algorithms, agent-based simulation, and multimodal simulation, are addressed in only a cursory fashion. This paper proposes a possible structure for a transportation system simulation manual that would cover the limitations and gaps in the existing literature. The proposed document would consist of five volumes: concepts, model building, verification and validation, results analysis, and case studies and supplementary materials.