Chronic wasting disease (CWD) is a fatal neurodegenerative disease in cervids which is caused by prions, and new cases continue to appear in populations in North America and globally. The United States Department of Agriculture-approved tests for diagnosing CWD use obex and/or retropharyngeal lymph nodes, which are challenging to collect as the tissues require anatomical knowledge, skill, and time to dissect. Third eyelids contain lymphoid follicles and are easier to collect. We determine whether third eyelids from naturally infected white-tailed deer are a reliable tissue for detecting CWD prions using real-time quaking-induced conversion (RT-QuIC), if positive results can be confirmed by immunohistochemistry, and if the results are reproducible between laboratories. Testing of third eyelids individually by RT-QuIC had a sensitivity of 94% and a specificity of 100%, and pooling of 5 third eyelids into one sample yielded a sensitivity of 100% and a specificity of 100%. Although IHC on third eyelid can be used in conjunction with RT-QuIC to support a positive diagnosis, using IHC on third eyelids in isolation should be performed with caution as additional validation for this tissue type is recommended. Our results support that testing third eyelids is a potentially more efficient way for management agencies to improve and expand their CWD surveillance.