Free-living amoebas (FLA) are protozoan parasites that occasionally cause disease in humans after contact with contaminated water or soil. We describe a series of three cases of encephalitis in a family group with a fatal outcome that occurred in the Tumbes region between December 2019 and February 2020. Acan-thamoeba sp. was identified in the cerebrospinal fluid sample from case 1. All three cases had a history of entering a swimming pool months before the disease. In the Tumbes region there is no previous record of encephalitis due to FLA and its occurrence in a family cluster has never been reported before.