Infective endocarditis owing to Mycobacterium abscessus infection is rarely reported. Most cases of infective endocarditis caused by Mycobacterium abscessus are seen in patients after valve replacement. Although early surgical intervention is recommended and medical treatment with antibiotics according to the susceptibility to the pathogen, such as amikacin, imipenem, cefoxitin, quinolones and macrolides, are applied, the course of such endocarditis is usually subacute and often has fatal outcomes. The present case was a 29-year-old male patient who was an intravenous drug user who had recurrent endocarditis caused by Mycobacterium abscessus. Unusually, our reported case was infected on his native valve. However, we experienced recurrence despite antimicrobial therapy. For culture-negative endocarditis, physicians should consider the possibility of Mycobacterium abscessus infection and related treatment difficulties.