The objective of the study was to analyse and present the surgical management strategy for major skin flap complications (MSFC) after cochlear implantations. Patients fitted with a titanium-silicone-coated implant of the same kind, operated on between 1994 and 2013 with a standardised procedure (1076 medical charts) were analysed. Analysis aimed to identify and study individuals with skin problems related to the cochlear implant treatment, i.e. requiring surgical treatment in hospital defined as MSFC and focused on incidence, risk factors and treatment of MSFC. MSFC were diagnosed in 1.76 % of patients: 2.06 % of children and 1.35 % of adults, 2.43 % after implantation with a long “C”-shaped incision and 1.28 % after short retroauricular incision. Registered risk factors included head trauma, acute otitis media, poor hygiene in children, and general comorbidities in adults. The primary intervention was dependent on skin complication severity and included revision surgery with wound closure over an implant (52.6 %) and revision surgery with explantation (47.4 %). Revision surgery without explantation was successful in 40 % and the most effective approach was debridement with a two-layer rotational flap. Explantation led to ultimate wound healing in all cases. Major skin flap complications after cochlear implantation are rare, but their treatment is complex and difficult. Revision surgery with resection of infected tissue, formation of a rotational two-layer flap preceded and supplemented by intensive targeted antibiotic therapy can be effective and should be the first treatment option. Spontaneous implant explantation, abscess formation or unsuccessful primary treatment necessitate implant removal as the ultimate solution.