Polymicrobial endocarditis is uncommon, and polymicrobial endocarditis in combination with Coxiella burnetii is very rare. We herein describe an extremely rare case of polymicrobial bivalvular endocarditis due to coinfection with Enterococcus faecalis and Coxiella burnetii in a 62-year-old male patient, and extensively review the relevant medical literature. To the best of our knowledge, only three similar cases have been previously reported. Q fever is a worldwide endemic bacterial zoonosis, but it and its most common chronic complication, endocarditis, are still underestimated and underdiagnosed worldwide. This situation reflects the paucity of reported cases of polymicrobial endocarditis in combination with Coxiella burnetii. Clinical presentation of Q fever endocarditis is highly nonspecific, and diagnosis may be delayed or missed, leading to severe and potentially fatal disease. Our case and the previously reported similar cases emphasize the need for further evaluation of infective endocarditis due to Coxiella burnetii, in all cases of culture-negative endocarditis, and in prolonged oligo-symptomatic inflammatory syndrome, particularly in the presence of valvular heart disease. This approach should be applied even when typical pathogens are isolated, especially in endemic areas of Q fever, and with atypical presentation.