The concept of eHealth literacy refers to the ability of a person to access electronic health information, evaluate the information, and apply the resulting knowledge to address or solve a health problem. Considering the uncertainties and the subjective nature of e-health literacy, determining the levels of students’ e-health literacy is a complex problem. The aim of this research is to develop and implement a fuzzy expert system to determine the level of eHealth literacy anytime and anywhere without accessing the experts personally. Thus, after studying the different methods of measuring people’s literacy level, the Digital Health Literacy Instrument was chosen for developing the system. Its reliability and validity were evaluated based on the experts’ judgment and by asking for the participation of 50 university students. The implementation of the fuzzy expert system showed that the proposed system succeeded in 88% of analyzed cases. Moreover, to decrease the number of rules systematically to help with expert fatigue while responding to surveys, the fuzzy expert system was modified based on rough set theory, which caused a reduction in the number of rules from 432 to 200. The comparison between the two fuzzy expert systems demonstrated that no significant difference was detected and the modified system.