A relationship may exist between selenium and kidney calculi, but there is a lack of research in this field at present. Our study explored the relationship between the serum selenium level and a medical history of adult kidney calculi. We utilized data from the National Health and Nutrition Examination Survey conducted between 2011 and 2016. Participants self-reported their history of kidney stones, while serum selenium levels were measured using inductively coupled plasma dynamic reaction cell mass spectrometry. Our findings indicate a negative correlation between serum selenium levels and the risk of kidney stone history. In the multiple-adjusted model, the lowest serum selenium level group had a higher risk than the other groups. The odds ratio (95% confidence interval) of ever having kidney stones for the highest serum selenium level group was 0.54 (0.33–0.88). In the results of stratified analysis, this relationship was still significant in the groups of women and those 40–59 years. We also found that as a nonlinear dose–response relationship between serum selenium levels and the history of kidney stones disease. In our research, we found that people with higher serum selenium levels had a lower risk of having a history of kidney stones. We concluded that selenium may have a protective effect on kidney stones. In the future, more population studies are needed to explore the relationship between selenium and kidney stones.