The ever-changing social implications of the COVID-19 pandemic have resulted in an urgent need to understand the working environments and health status of workers. We conducted a nationwide Internet-based health survey of Japanese workers in December 2020, in the midst the country's "third wave" of COVID-19 infection. Of 33,087 surveys collected, 6,051 were determined to have invalid responses. The 27,036 surveys included in the study were balanced in terms of geographical area, sex of participants, and type of work, according to the sampling plan. Men were more likely than women to have telecommuted, while women were more likely to have resigned since April 2020. Forty percent and 9.1% of respondents had a K6 score of 5 or higher and 13 or higher, respectively, and they did not exhibit extremely poor health. The present study describes the protocol used to conduct an Internet-based health survey of workers and a summary of its results during a period when COVID-19 was spreading rapidly in Japan. In the future, we plan to use this survey to examine the impact of COVID-19 on workers' work styles and health.