Protein S deficiency (PSD) is an inherited or acquired disorder associated with an increased risk of thrombosis. We describe the unusual case of a previously healthy 45-year-old man with PSD. The patient was admitted for work-up of hematochezia and was diagnosed with colorectal cancer. Preoperative evaluation was unremarkable, and he subsequently underwent an uneventful laparoscopic total colectomy. The next day, he complained of chest tightness, and a computed tomography enterography revealed acute thrombosis throughout the entire superior mesenteric vein. Further laboratory evaluation revealed decreased free protein S levels. Polymerase chain reaction and direct sequencing of the PROS1 gene revealed a heterozygous transition (NM_000313.3 c.1907A > G), resulting in an amino acid change (p.Tyr636Cys). Although several case reports have described mesenteric venous thrombosis (MVT) in individuals with PSD, most have just reported decreases in the activity or concentration of protein S. We confirmed a nucleotide alteration of PROS1 associated with PSD. This patient, who had hereditary thrombophilia, may have developed MVT after transient exposure to abdominal surgery. We may need to implement more comprehensive coagulation testing prior to surgery considering the prevalence and possible risk of thromboembolic event.