Goeldi studied zoology in Jena, Germany with Ernst Haeckel, and in 1884 he was invited by Ladislau de Souza Mello Netto, the influential director of the Brazilian Museu Imperial e Nacional, to work at that institution.

In May 1890, he was fired, due to political circumstances related to the proclamation of the republic and the exile of his principal benefactor, Emperor D. Pedro II.

In 1905 Émil Goeldi renounced his post, due to ill health, and returned to Switzerland where he died in Bern, in 1917, at age 58.

Some of the species which bear his name are: Several other species were named in honour of Émil Goeldi, such as: Goeldi was also recognized as an important early figure in public health and epidemiology in Brazil, because he studied the mechanism of transmission of yellow fever and advocated the importance of fighting the mosquito as the vector of the disease, several years before Oswaldo Cruz did so.

His extensive scientific research on the geography, geology, flora, fauna, archaeology, ethnography and socio-economical conditions of the present day region of Amapá was very important to end the Contestado territorial litigation between France and Brazil, ceding the territory to Brazil on 1 December 1900, by the international decision of the court of Bern.