Khojaev was born in to a family of wealthy traders. He was sent to Moscow by his father in 1907. There he realized the tremendous gap between contemporary European society and technology, and the ancient, tradition-bound ways of his homeland.
He joined the Pan-Turkist Jadid movement of like-minded reformers in 1916, and, with his father’s fortune, established the Young Bukharan Party. Seeing the Russian Revolution as an opportunity, the Young Bukharan Party invited the Bolsheviks of the Tashkent Soviet to seize Bukhara by force in 1917. When this attempted invasion failed, Khojaev was forced to flee to Tashkent, and was only able to return after the Emir of Bukhara fled in September 1920.
Appointed head of the Bukharan People's Soviet Republic, he barely escaped assassination by Basmachi leader Enver Pasha. With the reorganization of Central Asia and subsequent purge of suspected Uzbek nationalists in 1923-1924, Khojaev rose to become President of the Council of People’s Commissars of the Uzbek Soviet Socialist Republic. However, he opposed Joseph Stalin’s heavy-handed control, particularly in the matter of cotton monoculture.
Khojaev was arrested on trumped up charges in 1937, tried in Moscow as a "Trotskyite and a Rightist" and executed on March 13 1938. Officially rehabilitated in 1966, he remains a controversial figure in modern Uzbekistan. On the one hand, he is seen as a traitor who sold his country and people into Soviet servitude. On the other hand, he is seen as an idealist, who sought modernization and independence for Turkestan, but was caught up in forces beyond his control.
There are few monuments to him in modern Uzbekistan, and although his father’s house in Bukhara is preserved as a monument, it is styled as "House of a Wealthy Local Merchant", with very little emphasis on Khojaev himself.