Outbreaks of infectious diseases can occur after natural disasters as vital services are disrupted and populations move into evacuation centres. National notifiable disease surveillance may be inadequate in these situations because of resource-consuming disease confirmation or system interruptions. Although syndromic surveillance has been used as an alternative in post-disaster situations, no systematic evaluations of it have been published. We evaluated the ad hoc paper-based syndromic surveillance system implemented in evacuation centres in Ibaraki prefecture after the 2011 Great East Japan Earthquake and Tsunami. We assessed the simplicity, acceptability, data quality, timeliness and portability of this system and reviewed its usefulness. We concluded that the system was simple, acceptable, portable and useful. The documentation and monitoring of disease events and trends were useful for developing interventions in evacuation centres and have since been used to improve post-disaster infectious disease and surveillance knowledge in Japan. We believe timeliness was a challenge due to the chain of data transmission and communication passing through an intermediary. Future implementations of this system could consider a more direct chain of data transmission and communication from collectors to analysers. Too few key informant interviewees and the inability to obtain original paper-based data from evacuation centres limited our findings; we conducted this evaluation four years after the response occurred. Future evaluations should be completed closer to when operations cease. The usefulness of the system suggests adopting it in future disasters. A simple, plain-language manual should be developed to improve future employment.