Emerita rathbunae is found on the shores of the eastern Pacific Ocean, from the southern end of the Gulf of California in Mexico to Iquique in northern Chile, including the Galápagos Islands. In the south of its range, E. rathbunae co-occurs with the southern population of E. analoga, which occurs as far north as mainland Ecuador.
Despite their sympatry, the closest relative of E. rathbunae is not E. analoga; rather, E. rathbunae is part of a clade that also includes species from the western Atlantic Ocean, including E. portoricensis and E. benedictii. The last common ancestor of the genus is thought to have lived in the Pacific Ocean, and to have colonised the Gulf of Mexico when the Isthmus of Panama was submerged, and E. rathbunae is thought to have similarly recolonised the Pacific from ancestors that lived on the Atlantic side of the Isthmus of Panama.