On his arrival at the region's only airport, the Aga Khan was given the traditional welcome -- he was offered salt and bread.
Later in the region's capital, Khorog, schoolchildren waved flowers and chanted songs in his honour.
The Ismaili community like other groups in Tajikistan has been severely affected by the civil war which followed independence.
But the Aga Khan has provided large amounts of food aid to the remote region, which the BBC Central Asia correspondent says saved many from virtual starvation.
From the newsroom of the BBC World Service