The visit comes amid escalating economic pressures from the West and warnings about safeguarding oil shipments from possible Iranian blockades.
The findings from the mission could greatly influence the direction of U.S.-led efforts to rein in Iran's ability to enrich uranium, which Washington fears could eventually produce weapons-grade material.
Iran has declined to abandon its enrichment labs, but claims it only seeks to fuel reactors for energy and medical research.
The International Atomic Energy Agency team will likely visit an underground enrichment site in the city of Qom, about 80 miles south of Tehran. The site is carved into a mountain as a protection from possible airstrikes.
Before his arrival, IAEA's Deputy Director General Herman Nackaerts said he wants Tehran to "engage us on all concerns."
Iran has refused to discuss the alleged weapons experiments for three years, saying they are based on "fabricated documents" provided by a "few arrogant countries" - a phrase authorities in Iran often use to refer to the United States and its allies.
The Associated Press contributed to this report.