The mosque named after Hazret-Hyzr, an Islamic saint and eternal wanderer, stands on the southern slope of the Afrasi-ab hill, on the crossroad beside the central bazaar. A legend says that Hazret-Hyzr helped the patron of Samarkand Kusam ibn Abbas to escape and become never-dying.

 Once, there was a heathen temple which idols were broken in the first years of Islam. The temple was converted into mosque. Hazret-Hyzr was esteemed as a saint giving richness and good luck in far voyages and trade. Khazrat-Khizr Mosque is one of the ancient edifices of Samarkand was destroyed by Genghis Khan's hordes. It was rebuilt in 19 century.

Today's mosque was built on the medieval foundations in 1854. Carved ganch and coloured paintings on the ceiling decorate the interior.