The objective of the present study was to investigate the expression of S100B protein in serum of patients with brain metastases from small cell lung cancer (SCLC), and its clinical significance. A total of 138 patients with SCLC were selected from June 2013 to December 2015. Simultaneously, 138 healthy adult volunteers (healthy controls) were selected in the medical examination center of People's Hospital of Rizhao. Among the 138 patients with SCLC, 48 had liver metastases and 44 had brain metastases. Of the remaining 46 patients, 20 were initially diagnosed with SCLC and 26 underwent surgery and postoperative chemotherapy. The levels of serum S100B in patients and healthy controls were measured by ELISA, and analyzed by SPSS 20.0 statistical software. The serum S100B protein levels in patients with SCLC were significantly higher than those in healthy controls (p<0.05). Among the subgroups of patients with SCLC, the levels of serum S100B in patients with brain metastases were significantly higher than in the other subgroups (p<0.05). No significant differences were found between the other subgroups, except for the brain metastases group. We found that serum S100B protein expression levels were significantly reduced in patients with brain metastases after cobalt-60 radiotherapy (p<0.05). During follow-up, we found that higher expression of S100B protein was usually associated with poorer prognosis, higher mortality rate at 1 year, and lower survival rate. In conclusion, S100B protein can serve as a serological marker for brain metastases from SCLC, which provides important theoretical support for early detection of brain metastases.