Introduction: Transient tooth discoloration (TTD) is an endodontic condition associated with dental traumatic events. To the best of the authors’ knowledge, this is the first case report of transient coronal discoloration of the two upper permanent central incisors following periodontal instrumentation of root surfaces affected by aggressive periodontitis. The initial case presentation and multi-disciplinary periodontal, endodontic, and orthodontic management are described. Case Presentation: A 17 year-old male was referred from the Orthodontics Department to the Periodontics Department at the Oral Health Center of Western Australia. A localized aggressive periodontitis was diagnosed. After meticulous periodontal debridement of the mid-root and apical root portions of two upper central incisors, TTD was noted five months later. The diagnosis, case management and biological explanations for the unique presentation of these conditions are discussed. Conclusion: Transient tooth discoloration may be caused by trauma from periodontal instrumentation. This is the first report of TTD in an aggressive periodontitis case. Proper diagnosis and management of this particular condition is important to protect the integrity of the pulp in affected teeth. This case report opens the possibility of the presence of transient tooth discoloration originating from causes other than traumatic luxation or intra-alveolar root fractures of teeth.