Infective endocarditis retains high morbidity and mortality rates despite recent advances in diagnostics, pharmacotherapy, and surgical intervention. Risk stratification in endocarditis patients, including blood-culture negative endocarditis, is crucial in deciding the optimal management strategy; however, the studies investigating risk stratification in these patients were lacking despite the difference with blood-culture positive endocarditis. The aim of this study is to identify risk factors associated with in-hospital mortality in blood-culture negative infective endocarditis patients. A retrospective cohort study was conducted at National Cardiovascular Center Harapan Kita, Jakarta in blood-culture negative infective endocarditis patients from 2013 to 2015. Patient characteristics, clinical parameters, echocardiographic parameters, and clinical complications were collected from medical records and hospital information systems. There were 146 patients that satisfy the inclusion and exclusion criteria out of 162 patients with blood-culture infective endocarditis. The in-hospital mortality rate was 13.5%. On bivariate analyses, factors that were related to in-hospital mortality include New York Heart Association (NYHA) class III and IV heart failure (p = 0.007), history of hypertension (p = 0.021), stroke during hospitalization (p < 0.001), the decline in renal function (p < 0.001), and surgery (p = 0.028). Variables that were independently associated with mortality upon multivariate analysis were heart failure NYHA functional class III and IV (OR 7.56, p = 0.011), worsening kidney function (OR 10.23, p < 0.001), and stroke during hospitalization (OR 8.92, p = 0.001). Presence of heart failure with NYHA functional class III and IV, worsening kidney function, and stroke during hospitalization were independently associated with in-hospital mortality in blood-culture infective endocarditis patients.