Purpose To investigate the outcomes of a combined treatment regimen comprising primary surgery and tyrosine kinase inhibitor (TKI) therapy for synchronous metastatic gastrointestinal stromal tumors (GIST). Methods We analyzed retrospectively 14 cases of synchronous metastatic GIST from the Kinki GIST registry between 2003 and 2007. Results The primary tumor was located in the stomach, small intestine, and rectum in seven, six, and one patients, respectively. Metastatic tumors developed in the liver, peritoneum, other sites, and multiple organs in three, six, two, and three patients, respectively. The R0 resection rate was 42.9 % and the 5-year overall survival rate was 69.3 %. There was no significant difference in the 5-year overall survival rate between patients who underwent R0/R1 and those who underwent R2 resection (71.4 vs. 68.6 %). There was a strong correlation between survival time from diagnosis and the duration of imatinib therapy (Pearson’s correlation coefficient, 0.86; p  < 0.001). Conclusions Although the role of surgery in the treatment of synchronous metastatic GIST is still unclear, primary surgery as the sole frontline treatment may not have a survival benefit: Continuous TKI therapy is more important for prolonging survival.