His visit comes at a time when Iran is at the center of an international diplomatic standoff over it´s nuclear program.
A former nuclear program envoy himself, Larijani is expected to be pressed by Japan on the nuclear issue as Tokyo does with North Korea.
But, Japan relies heavily on Iranian oil and Tokyo is unlikely to press the issue as strongly as it tries with Pyongyang.
Western countries, and Japan, fear Iran wants to build nuclear weapons.
Iran says program is for peaceful purposes like generating electricity.
Earlier this month, Iran announced it plans to enrich uranium to 20 percent purity,
That´s the level needed to fuel a medical research reactor in Tehran.