They apparently cordially discussed the rule of law and the peace process.
It is the third public meeting between the military strong man and Suu Kyi. The meeting took place as Myanmar is in the process of presidential candidate nomination.
The army's commanders Lieutenant-Generals Mya Tun Oo and Ye Aung and the NLD's Dr Zaw Myint Maung and Dr Tin Myo Win attended the meeting.
The army leader and Suu Kyi first met on December 2 where they apparently agreed to cooperate for the benefit of the country and to ensure peace, stability, the rule of law, unity and development.
On January 25 the talks reportedly focussed on the transfer of power, parliamentary affairs, the formation of the new government and building last October's nationwide ceasefire agreement into a stable peace.
The NLD secured 886 seats in all parliaments: 255 in the Lower House, 135 in the Upper House, 475 in the regional and state parliaments and 21 ethnic seats.
The party can nominate a vice-president for each of the two houses and select one of them as president. The military will pick a third vice-president.
On March 17, MPs will hold meetings to select the vice-presidents, said Mahn Win Khaing Than, Speaker of the Union parliament.
President Thein Sein steps down on March 30.