Tsantsas, commonly referred to as “shrunken heads”, are unique and valuable antiquities that were produced by the Shuar, Achuar, Awajún/Aguaruna, Wampís/Huambisa, and Candoshi-Shampra (SAAWC) peoples until the mid twentieth century. Originally used with ceremonial purpose during important social group functions, tsantsas became monetarily valuable as keepsakes and curios during the nineteenth century as a result of Western/European cultural encroachment. Unmet demand resulted in the production of convincing forgeries that created confusion about the authenticity of existing collections. Ceremonial tsantsas are both human remains and valuable cultural items. Their production and purpose were negatively influenced by colonialism and the outside curio market; as such many institutions may choose to repatriate them to their places of origin. Herein, we report on the authentication and repatriation of a ceremonial tsantsa recently rediscovered in a university’s natural history collection. The personal memoirs of the original collector describe that it originated in the Ecuadorean Amazon. In consultation with the government of Ecuador, it was determined that authentication was required prior to repatriation. The tsantsa was compared to a list of thirty-three distinct characteristics shared by ceremonial tsantsas. These criteria were taken from those provided by Ecuador’s National Cultural Heritage Institute and those found in prior studies from the academic literature; they include notable skin and hair features, structure and facial anatomy, and evidence of traditional fabrication and modification. We were able to affirm 30 of the 33 authenticating indicators. As part of our protocol the tsantsa was scanned with a CT-imaging system. The resulting 3D images were invaluable in discerning subtle and difficult-to-visualize characteristics regarding the skin and patterns of modification, although there are limitations related to the small size of filamentous structures. The results of the authentication were accepted by the Ecuadorean government, and the tsantsa was repatriated in June 2019. An additional benefit of CT-imaging is that data files can be generated in order to create rapid prototypes via 3D printing. In fact, as our work demonstrates, artifacts of value can be repatriated while simultaneously preserved as a volumetric replica for the purposes of a collection.