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Objective This manuscript aims to provide an overview of the unique considerations and best practice principles associated with the manufacture of human viral challenge agents. Results Considerations are discussed on the entire process from strain and viral source selection through manufacturing, safety and efficacy testing. The human viral challenge (HVC) model is an important tool to help accelerate the drug development process but producing viruses suitable for use in the model presents a unique set of challenges. There are many case by case decisions and risk assessments to consider and no clear international standard to produce viruses for this purpose. The authors present challenge virus manufacturing considerations from the current literature, regulatory guidance and their own direct experience in producing challenge viruses. The use of these viral stocks in clinical studies, as published in peer-reviewed journals, is also briefly described. Electronic supplementary material The online version of this article (10.1186/s13104-018-3636-7) contains supplementary material, which is available to authorized users.