Baker will be just the sixth woman to be honoured in the secular temple to the “great men” of the French Republic, which sits on a hill in Paris’s Left Bank.
She will also be the first entertainer to be immortalised alongside the likes of Victor Hugo, Emile Zola and Marie Curie.
The “pantheonisation” of the world’s first black female superstar caps years of campaigning by Baker’s family and admirers to give her the rare posthumous honour.
President Emmanuel Macron granted the request in August to recognise the fact that Baker’s “whole life was dedicated to the twin quest for liberty and justice,” his office said last week.
Baker is buried in Monaco, where her body will remain.
During Tuesday’s ceremony a coffin containing handfuls of earth from four places where she lived — the US city of St. Louis where she was born; Paris; the Chateau de Milandes where she lived in southwest France; and Monaco — will be placed in the tomb reserved for her in the Pantheon’s crypt.
The coffin will be carried into the building by members of the French air force, commemorating her role in the French Resistance during World War II.
Macron will deliver a speech and some of Baker’s relatives will read short texts written by the trailblazing performer.
Baker’s name will also soon be added to the name of the Gaite metro station next to the Bobino theatre in southern Paris, where she last appeared on stage a few days before her death in 1975.
Born Freda Josephine McDonald into extreme poverty in Missouri in 1906, Baker left school at 13.
After two failed marriages — she took the name Baker from her second husband — she managed to land herself a place in one of the first all-black musicals on Broadway in 1921.
Like many black American artists at the time, she moved to France to escape racial segregation back home.
The woman nicknamed the “Black Venus” took Paris by storm with her exuberant dance performances, which captured the energy of the Jazz Age.
One of the defining moments of her career came when she danced the Charleston at the Folies Bergere cabaret hall wearing only a string of pearls and a skirt made of rubber bananas, in a sensational send-up of colonial fantasies about black women.
The performance marked the start of a long love affair between France and the free-spirited style icon, who took French nationality in 1937.
At the outbreak of World War II, she joined the Resistance against Nazi Germany, becoming a lieutenant in the French air force’s female auxiliary corps.
She also became a spy for France’s wartime leader-in-exile General Charles de Gaulle, obtaining information on Italian leader Benito Mussolini and sending reports to London hidden in her music sheets in invisible ink.
“France made me who I am,” she said later. “Parisians gave me everything… I am prepared to give them my life.”
She also waged a fight against discrimination, adopting 12 children from different ethnic backgrounds to form a “rainbow” family at her chateau in the Dordogne.
She died on April 12, 1975, aged 68, from a brain haemorrhage, days after a final smash-hit cabaret show in Paris celebrating her half-century on the stage.
She is the second woman to be entered by Macron into the Pantheon, after former minister Simone Veil, who survived the Holocaust to fight for abortion rights and European unity.
In a sign of the universal affection in which Baker is still held in France, there was no public criticism of the decision to honour her, including from far-right commentators that are generally scathing of anti-racism gestures.