Mohammad Hassan al-Bahrani, Aljazeera's Tehran bureau chief said on Thursday: "We have reopened since June 17, following negotiations between Aljazeera directors and Iranian authorities."
Aljazeera was thrown out of the country in April 2005, after accusations by the Iranian government that it was stirring up ethnic violence in its coverage of clashes between ethnic Arabs and security forces in the country's southwestern Khuzestan province.
Three people were killed and 200 arrested in clashes in the oil-rich province, which borders Iraq.
About 3% of Iran's 67 million people are Arabs, many of whom reside in Khuzestan, home to vast oilfields which account for 80% of the country's oil export profits.
The country's western border is comprised of several ethnic groups including Arabs, Kurds and Azeris, which has led to ethnic tensions in the past.
A series of bomb attacks in June last year against government buildings in the province also left seven people dead.