The government said in a statement that the operation will take place with "dignity and respect", and in the presence of the Franco family.
Works to remove Franco's remains will begin at 10.30 a.m. on Thursday. Both the exhumation and reburial will take place privately, in the presence of family members.
Justice Minister Dolores Delgado will attend on behalf of the royal household.
His body lies under the floor at the foot of the main altar in the basilica within the Valley of the Fallen - the colossal monument that is a controversial symbol of the military dictatorship that took hold in Spain after the Civil War (1936-39).
The government of Socialist Prime Minister Pedrp Sanchez decided to remove the dictator's remains, despite legal push-back from Franco's grandchildren.
About 34,000 people who died on both sides of the conflict are also buried at the complex outside of Madrid.
Franco died in November 1975 after a series of illnesses, having ruled Spain with an iron fist for four decades.
The 492-foot granite cross towering over the complex can be seen from several miles away, which many Republican survivors, their relatives and democratically-minded citizens consider offensive.
It is considered the only state-endorsed mass pilgrimage site remaining in Europe after the end of World War II.