Amid tight security and in virtual secrecy, his coffin will be taken from the Valley of the Fallen and reburied in a private family vault, transported either by helicopter or, if bad weather intervenes, by guarded motorcade.
"It's intensely symbolic for Spain," said political scientist Pablo Simon, "because the (Franco) monument has always been connected to those who miss the old regime."
With media prohibited, the exhumation ceremony will be witnessed by a select few: Justice Minister Dolores Delgado, a forensics expert, a priest, and 22 of Franco's descendants.
They include his oldest grandson Francisco Franco, who labelled the operation - and its low-key nature - a political ploy by the governing Socialist Party.
"I feel a great deal of rage because they have used something as cowardly as digging up a corpse, using a body as propaganda and political publicity to win a handful of votes before an election," he told Reuters late on Wednesday.
In government since mid-2018 and facing a national election next month, the Socialists have long sought to exhume Franco, who unleashed the civil war that killed around 500,000 people between 1936 and 1939.
They won backing for the decision to move his remains from a divided parliament, and the Supreme Court ratified it last year after dismissing a challenge from Franco's descendents.
The government estimates the move will cost up to 63,000 euros ($70,000).
"Exhuming the dictator's body suggests that the Valley of the Fallen's significance could be reclaimed, a normal process within democracies like ours," Simon said.