This case report presents a treatment of peri-implantitis associated with a pre-existing pathology. Peri-implantitis around implant #19 was detected from pus discharge upon probing. Guided bone regeneration was performed to treat the peri-implantitis with the administration of antibiotics. The histopathologic evaluation of soft tissue taken from the circumferential defect around the implant exhibited a cyst. The postsurgical CBCT and the follow-up radiograph confirmed the maturing bone graft and a reduced size of the defect around the implant.