Emajõe is a genitive form of Emajõgi, a river in Estonia and may refer to:
Emajõe-Suursoo Nature Reserve Emajõe Business Centre in Tartu Emajõe Summer Theatre Emajõe tänav, street in Tartu Liis Emajõe (born 1991), Estonian footballer Riin Emajõe (born 1993), Estonian footballer