The number of complications related to dental implants has been increasing, as implant therapy has grown to become the most popular treatment choice for replacing missing teeth. Various cases of implant complications have been reported, particularly biologic complications caused by inadequate surgical techniques, including malpositioned implants, that are difficult to solve. In the present case, two malpositioned implants with peri-implantitis were placed in the maxillary right first molar area of a 64-year-old woman. To treat the peri-implant infection and facilitate self-plaque control, one malpositioned implant was removed, and the other was treated with open flap debridement using an erbium-doped yttrium aluminum garnet (Er:YAG) laser. The implant suprastructure was then changed adequately to recover oral function. This case report demonstrates the clinical steps, healing process, and 6-month follow-up of peri-implantitis caused by malpositioned implants.