Bacteremia is one of the most common manifestations of invasive pneumococcal disease (IPD). One complication of bacteremia is endocarditis; yet, few studies have evaluated the overall incidence and risk factors for IPD-associated endocarditis. Thus, we evaluated the overall incidence and risk factors of endocarditis compared to those without endocarditis in a large population of IPD patients. We prospectively collected all IPD cases from 2000 to 2014 in Northern Alberta, Canada. Descriptive statistics were used to compare sociodemographic variables, clinical characteristics, and IPD-related outcomes between patients with and without endocarditis. Endocarditis complicated the course of only 28 (0.3%) of 3251 adult patients with IPD. Endocarditis patients were more likely to use illicit drugs and have a higher severity of illness at presentation (i.e., higher rate of altered mental status and rate of intensive care unit [ICU] utilization, p < 0.05); however, no other major risk factors were identified. New murmur development among endocarditis patients was common: 39.3% compared to 2.2% of non-endocarditis patients (p < 0.001). The mortality rate of 39.3% was more than twice that of the rate of 14.7% for the patients with IPD but without endocarditis. There was no pneumococcal serotype predilection for endocarditis. Endocarditis is an uncommon complication of IPD, but, when present, is associated with a significantly increased risk of mortality. Overall, few specific risk factors were identified for IPD-related endocarditis, with the exception of illicit drug use.