The Palace of Princess Fatima, the daughter of Khedive Ismail, was chosen to be remodeled to house the museum, and construction of the museum started in November 1930.[citation needed] During the planning of the museum the director of Hungary's Royal Agricultural Museum directed the work. A Hungarian national, Ivan Nagy, was the first director of the museum which was opened in 1938.

The museum is made up of separate museums: the museum of Ancient Egyptian agriculture; museum of scientific models; museum of plant wealth; Syria museum; the Greek, Roman, Coptic, and Islamic museum; and the cotton museum.