Even in the middle of an epidemic of a very serious illness, outbreaks of other infectious diseases will continue. Clinicians need to be able to make rapid decisions about the nature of the outbreak and how to manage it. A balance needs to be struck between managing all patients as if they have the worst-case scenario illness and the resultant risks to themselves, their colleagues and the mission. This paper reviews basic epidemiological tools that inform robust decision-making in the management of such outbreaks. It then describes how a pragmatic approach, combined with effective use of these techniques, rapid diagnostics and remote specialist support, allowed a large outbreak of gastroenteritis to be safely and effectively managed during the response to the Ebola virus disease epidemic in Sierra Leone.