Background. Infective endocarditis (IE) is an uncommon but life-threatening infection. It is commonly associated with diseased or damaged valves. Patients with congenital heart disease are more prone to getting IE than the general population. The typical organisms that cause IE include Staphylococcus , Coagulase-negative Staphylococcus, Streptococcus viridians and Enterococci. However, the importance of rare micro-organisms like Kocuria kristinae should not be underestimated especially when isolated from multiple blood cultures in patients suspected of IE. Case presentation. We report a rare case of right-sided infective endocarditis due to K. kristinae in a young non-diabetic, non-addict female of low socioeconomic class who presented with undiagnosed fever for 1 year. She was investigated and treated for fever by several general practitioners without relief. Later on, she was diagnosed by a local cardiologist to have perimembranous ventricular septal defect with a small pulmonary valve vegetation. She was referred to a tertiary care cardiac hospital in Rawalpindi, Pakistan for further management. Transthoracic and transesophageal echocardiography confirmed IE secondary to preexisting congenital heart disease complicated with a small pulmonary vegetation. Her blood cultures yielded growth of K. kristanae, a rare micro-organism to cause IE. The patient responded to the antibiotic therapy. Conclusion. Clinicians should have a high index of suspicion for K. kristanae IE as a possible cause of a prolonged fever especially in the presence of congenital heart disease. Antibiotic susceptibility is required for adequate therapy.