Purpose Splanchnic vein thrombosis (SpVT) in solid tumors has not been well investigated. Therefore, the treatment guidelines for SpVT are not well established. We aimed to conduct this prospective study to investigate the clinical characteristics and risk factors influencing survival in patients with gastrointestinal cancer with SpVT. Materials and methods Fifty-one patients with gastrointestinal cancer diagnosed with SpVT were prospectively enrolled. The clinical characteristics and courses of SpVT were analyzed. Results SpVT occurred in various clinical situations (at the time of initial cancer diagnosis or tumor recurrence after curative therapy, in the postoperative period, during chemotherapy, or in the period of end-of-life care). Among the total patients, 90.2% had no SpVT-related symptoms at initial SpVT diagnosis, and 82.4% did not receive any anticoagulation therapy. The clinical course of SpVT during the follow-up varied: (1) spontaneous resorption without any anticoagulation (47.1%), (2) resorption with anticoagulation (3.9%), (3) persistent thrombosis without progression (17.6%), and (4) SpVT extension (31.4%). Although the SpVT showed extension in some cases, most of them did not cause symptoms or had little impact on the patient’s cancer treatment course. During the follow-up period, 23 patients died, all of which were caused by tumor progression. In the multivariable analysis, performance status and clinical situation at the time of SpVT diagnosis were significant prognostic factors. Conclusions Clinicians could adopt a strategy of close observation for incidentally detected SpVT in patients with gastrointestinal cancer. Anticoagulation should be considered only for SpVT cases selected strictly, weighing the risks and benefits.