In patients with chronic kidney disease (CKD), coronavirus disease 2019 (COVID-19) has a higher mortality rate than the general population; therefore, prevention is vital. To prevent COVID-19 infection, it is important to study individuals’ risk aversion behavior. The objective of this study was to understand how the behavioral characteristics of physical distancing, hygiene practice, and exercise changed in patients with CKD during the COVID-19 pandemic and to identify the characteristics of patients who showed weakened or strengthened behavioral changes. We analyzed data from the Study on Kidney Disease and Environmental Chemicals (Clinical Trial No. NCT04679168), that examined a prospective cohort of patients with CKD. This cohort included patients with CKD who visited the participating hospitals for the first time between June and October 2020 and the second time between October 2020 and January 2021. Data on demographics, socio-economic details, and behavioral characteristics were collected through a questionnaire survey. Using a multivariable logistic regression model, we identified whether COVID-19 infection risk perception and previous strong behavioral changes affected behavioral changes during the first and second visits. A total of 277 patients (33.2% females) were included in the analysis. Nine out of 12 behaviors were reinforced at the first visit, and five out of nine reinforced behaviors were weakened at the second visit. A high-risk perception of COVID-19 infection was not associated with the tendency of overall behavioral reinforcement or maintaining behaviors in an enhanced state at the second visit. Strong behavioral changes at the patients’ first visit to the hospital were associated with a tendency to strengthen or maintain reinforced behaviors at the second visit (adjusted odds ratio 1.99, 95% confidence interval 1.19–3.34; P = 0.009). Even if the initial COVID-19 risk perception is high, behavioral changes worsen over time. Individuals who showed more active behavioral changes at the beginning of the COVID-19 pandemic tended to maintain reinforced behavior over time. Continuous education and monitoring are needed to maintain changed behaviors, especially in patients with a high initial COVID-19 risk perception.