The meeting was one of the conditions set by the EU representatives for agreeing to travel to Rangoon.
It is reported to be only her second diplomatic contact in more than four months.
The meeting was one of the conditions set by the EU representatives for agreeing to travel to Rangoon.
The four-day visit, which began on Sunday, is aimed at breaking the deadlock between the Burmese Government and Aung San Suu Kyi's National League for Democracy (NLD).
The NLD won by a landslide in the 1990 general election, but the military has refused to hand over power.
Dialogue
On Monday, the EU delegation began talks with the country's military government to urge them to move towards democracy. It met Lieutenant-General Khin Nyunt, the powerful head of military intelligence.
Earlier this month, the United Nations revealed Aung San Suu Kyi and senior government leaders had held secret meetings - the first between the two sides in six years.
The pro-democracy leader herself has not commented publicly about the talks, which are understood to have been with General Nyunt.
Celebrations
The EU is maintaining sanctions against the country because of persistent human rights violations by the regime.
Asian and Western governments have welcomed the EU visit, but many observers remain sceptical that a major breakthrough is in the offing.
Nevertheless, there is a new mood of optimism in Burma and at the NLD's headquarters in Rangoon.
Last week, the military released 84 NLD members of from detention.
And the media's repeated attacks on Aung San Suu Kyi have recently stopped.
Malaysia's Prime Minister Mahathir Mohamad, fresh from a visit to the country, also said in a newspaper article published on Sunday that the ruling junta was willing to hold elections in a few years.
Aung San Suu Kyi's only other diplomatic contact since September, has been with UN special envoy Razali Ismail, who met her on two mediation missions in October and January.