Splanchnic vein thrombosis (SVT), which is particularly prevalent in myeloproliferative neoplasms (MPNs), has a multifactorial pathomechanism involving the anticoagulant protein C (PC) pathway. To better characterize the hypercoagulable state in SVT we assessed its key enzymes thrombin and activated PC (APC). The study population included 73 patients with SVT, thereof 36 MPN+, confirmed by bone marrow biopsy, 37 MPN−, and 30 healthy controls. Direct measurement of the active enzyme forms of thrombin and APC in the circulation was achieved by using oligonucleotide-based enzyme capture assays (OECA). Additionally, activation markers of coagulation and fibrinolysis were measured. Plasma levels of free thrombin and APC were higher in the MPN+ than in the MPN− cohort, with 0.49 vs. <0.46 pmol/L (p = 0.0057), respectively, 1.23 vs. 0.58 pmol/L (p = 0.0122), and in healthy controls (vs. <0.46 pmol/L, p = 0.0012; vs. 0.54 pmol/L, p = 0.0035). The indirect activation markers prothrombin fragment 1+2, thrombin-antithrombin complex, and D-dimer did not differ between groups. Receiver operating characteristic analysis suggested that SVT patients with MPN can be better distinguished by APC than by conventional indirect thrombin markers. A potential application of these biomarkers to guide anticoagulant therapy and to investigate the role of the PC pathway in MPN-associated hypercoagulability should be further studied.