Pump thrombosis is associated with high morbidity and mortality in patients with a continuous-flow left ventricular assist device. Although it has been defined clearly, the diagnosis and treatment of this complication still remain controversial. Between 2010 and 2014, 163 consecutive patients (mean age: 50.7 ± 13 years, 84% males, median duration of support: 277 (2–1077) days) were implanted a continuous-flow left ventricular assist device. Prospectively collected data of all patients who had at least one pump thrombosis event have been analyzed, retrospectively. Twenty-one pump thrombosis events were observed in 15 patients (9.2%, 0.137 events/patient-year). Median duration of support at the time of first pump thrombosis event was 259 (8–585) days. Overall mortality was 40% (6/15), and overall procedural success was 71.4% (15/21) in our entire cohort. The cause of mortality was hemorrhagic stroke in those who had medical treatment (n = 5), and sepsis and right ventricular failure in the other who had pump exchange. Pump exchange was performed in five patients, of which four survived. Glycoprotein IIb/IIIa antagonists are not beneficial in medical treatment of pump thrombosis. Medical treatment methods including unfractionated heparin and thrombolytics may completely resolve the thrombus and save some patients from pump exchange. In patients where medical treatment does not result in complete thrombus resolution within a reasonable period, and a donor heart is not available, pump exchange is the ultimate solution. Further studies are needed for optimal dosing of thrombolytics to decrease the rate of side effects.