This is the second time the painting by the Dutch-born post-impressionist has been stolen from the Cairo museum.
Thieves made off with the canvas in 1978, before authorities recovered it two years later at an undisclosed location in Kuwait.
One year later, a duplicate was sold for $43m in London, sparking a debate in Egypt whether the returned painting was, in fact, a fake.
Authorities have never fully revealed the details of the first theft of the painting.
When it was recovered, Egypt's then-interior minister said three Egyptians involved in the heist had been arrested and informed police where the canvas was hidden.
Authorities never reported whether the thieves were charged or tried.
The one-foot-by-one-foot painting resembles a flower scene painted by the French artist Adolphe Monticelli, whose work deeply affected the young van Gogh.
The Monticelli painting also is part of the Khalil collection.