One of only two he ever painted of his friend and the only one whose whereabouts is known -- goes on sale next month with a price tag of up to 7 million pounds ($12.3 million).
The two men, among the greatest post-war British artists, were firm friends. But while Freud frequently sat for Bacon the latter returned the favor for only two portraits.
The first of the two portraits dating from 1952 has been missing since 1988 when it was stolen from an exhibition at Berlin's Neue Nationalgalerie.
Freud even went so far as to paint a wanted poster for the missing picture in 2001 but, despite some tantalizing tips, it has never been recovered.
'Lucian Freud and Francis Bacon are widely considered to be the most important British artists of the 20th century,' said Pilar Ordovas, head of contemporary art at auction house Christie's.
'We are thrilled to present to the international art market a rarely seen, intimate portrait which pays tribute to an inspirational friendship, and a key moment in the development of Freud's career.'
The portrait which goes on sale at Christie's in London on October 19 dates from 1956/7. As with the missing painting it shows Bacon with downcast eyes.
The two men sat knee-to-knee for the painting which captures an introspective expression on Bacon's face, and while Freud painted Bacon grumbled about the enforced lack of movement.
The painting is unfinished, showing only Bacon's face from forehead to chin. It is believed that he left abruptly when he finally rebelled against the strictures of the sitting.
The picture has been the property of the current owner since 1972 and has only rarely been seen in public -- in 2002/3 and 2005. It will go on show for the four days preceding the sale.
Images and text by Reuters