Thrombosis is the most common complication in BCR-ABL1 negative myeloproliferative neoplasms (MPN) that significantly impacts patients’ mortality. Generally, there is an agreement on risk factors that possibly contribute to the increased risk of thrombosis, including age, history of thrombosis, JAK2V617F mutation, and cardiovascular risk factors. This study retrospectively investigates MPN-related and patient-related variables in relation to the thrombosis occurrence in MPN. Our analyses show that JAK2V617F-mutated patients are at a significantly increased risk of thrombosis within five years before the MPN diagnosis point with a hazard ratio (HR) of 15.49 (P = 0.006). In multivariate analyses, independent risk factors for thrombotic complications during the follow-up are history of thrombosis (HR = 2.23, P = 0.019), age over 60 years at diagnosis (HR = 1.56, P = 0.037), the presence of JAK2V617F mutation (HR = 3.01, P = 0.002), and tobacco smoking (HR = 1.75, P = 0.01). Our results support the multifactorial mechanism of thrombosis in MPN patients, which demands individual and complex management.