The implant periapical lesion (IPL), a possible cause for implant failure, may occur from the presence of pre-existing microbial pathology such as endodontic/periodontal lesions. This case report presents a case history related to IPL, which was caused by a pre-existing endodontic lesion. In addition, other possible causes such as surgical trauma and the management strategies of IPL are suggested. For the treatment of the infected form of IPL, a sequential surgical therapy can be utilized. This includes surgical removal of the implant or implant apical region, thorough debridement of the infected lesion, systemic antibiotics, and/or guided bone regeneration. The implant therapy should be directed to minimize the occurrence or consequences of IPL by careful diagnosis, systematic treatment planning, and appropriate treatment procedures.