Background <p>Circulating long non-coding RNAs expression was associated with diagnosis and therapies of various diseases. The current study investigated the expression of lncRNA SLC9A3-AS1 in the serum samples from colon cancer patients and explored its potential functions in colon cancer cells.</p> Methods <p>Serum expression levels of SLC9A3-AS1 and miR-486 were measured in 130 patients with colon cancer and 96 healthy individuals using RT-qPCR. The influence of SLC9A3-AS1 expression and miR-486 expression on colon cancer cellular behaviors was detected by MTT assay and Transwell chamber assays. Pearson correlation analysis was used to analyze the association between SLC9A3-AS1 and miR-486.</p> Results <p>We found serum expression levels of SLC9A3-AS1 were overexpressed in sera of colon cancer patients. ROC curve analysis showed that SLC9A3-AS1 had a high area under the ROC curve value for early detection of colon cancer patients from a healthy control. The proliferation potential, migration, and invasion behaviors were weakened by si-SLC9A3-AS1 and reversed by the miR-486 inhibitor.</p> Conclusion <p>Serum SLC9A3-AS1 may be used as a non-invasive diagnostic predictor for the early screening of colon cancer. LncRNA SLC9A3-AS1 affects colon cancer cellular activities by negatively modulating miR-486. A major limitation of this study is the small sample size, and in addition, the lack of longitudinal data prevented us from conducting an in-depth analysis of long-term changes in variables.</p>