Thermal disinfection is probably the oldest water treatment method ever used. Similarly to other disinfection processes, it targets the inactivation of pathogenic (micro)organisms present in water, wastewater and other media. In this work, a pilot-scale continuous-flow thermal disinfection system was investigated using highly contaminated hospital wastewater as influent without any pre-treatment step for turbidity removal. The results proved that the tested system can be used with influent turbidity as high as 100 NTU and still provide up to log 8 microbial inactivation. Further results have shown energy consumption comparable to other commercially available thermal disinfection systems and relatively low influence on the investigated physical–chemical parameters.