Father Manuel Garcia Viejo was working in Sierra Leone with the Hospital Order of San Juan de Dios.
He was helping to fight the spread of the virus in Western Africa when he became ill.
A Spanish military plane was sent to take Father Viejo back to Spain from the Western city of Lunsar. He is the second priest from the country to pick up the illness.
Last month, Father Miguel Pajares, also a member of San Juan de Dios, died days after being diagnosed.
More than 2,600 people have died from Ebola. The virus is spreading across Guinea, Sierra Leone and Liberia, as well as Senegal and Nigeria.